From jrvalverde at cnb.uam.es Tue Mar 4 08:36:05 2003 From: jrvalverde at cnb.uam.es (José R. Valverde) Date: Tue, 4 Mar 2003 14:36:05 +0100 Subject: Jemboss app listing Message-ID: <20030304143605.3d72f6d6.jrvalverde@cnb.uam.es> Hi, I'm having trouble with Jemboss concerning the hierarchihcal listing of application menus in the top left side. This has been consistent for quite some time, and the problem is that the listing changes each time I start Jemboss. It seems like the Java application is getting an incomplete listing of applications, truncating the list at varying points each time Jemboss is started and offering an incomplete listing. It looks like a problem due to a short timeout waiting for the listing of applications.. Anyone knows if there is a fix for this? j From tcarver at hgmp.mrc.ac.uk Tue Mar 4 09:00:27 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Tue, 4 Mar 2003 14:00:27 +0000 (GMT) Subject: Jemboss app listing In-Reply-To: <20030304143605.3d72f6d6.jrvalverde@cnb.uam.es> Message-ID: Hi Jose What version of Jemboss/EMBOSS are you using and on what platform? I suspect this without authentication? Anyway you should find this is fixed in the currnet Jemboss release with EMBOSS-2.6.0. Regards Tim On Tue, 4 Mar 2003, Jos? R. Valverde wrote: > Hi, I'm having trouble with Jemboss concerning the hierarchihcal listing > of application menus in the top left side. This has been consistent for > quite some time, and the problem is that the listing changes each time I > start Jemboss. > > It seems like the Java application is getting an incomplete listing of > applications, truncating the list at varying points each time Jemboss is > started and offering an incomplete listing. It looks like a problem due > to a short timeout waiting for the listing of applications.. > > Anyone knows if there is a fix for this? From Wiepert.Mathieu at mayo.edu Tue Mar 4 14:17:15 2003 From: Wiepert.Mathieu at mayo.edu (Wiepert, Mathieu) Date: Tue, 4 Mar 2003 13:17:15 -0600 Subject: LINDNA Message-ID: <2F41CC6C9777D311ACBD009027B108EA0541C4FD@excsrv32.mayo.edu> Hi, I was looking at the lindna program, is there a program that can create the input files needed for this from a genbank or embl record? I saw the format needed for input, but couldn't find the program to create a file in that format, I thought seqret might do it? Thanks, -Mat From jmullersman at yahoo.com Tue Mar 4 14:43:38 2003 From: jmullersman at yahoo.com (Jerry Mullersman) Date: Tue, 4 Mar 2003 11:43:38 -0800 (PST) Subject: installation of Jemboss from EMBOSS-2.6.0 package questions Message-ID: <20030304194338.74089.qmail@web11606.mail.yahoo.com> I have been trying to install Jemboss in standalone mode from the EMBOSS-2.6.0 package on a Mandrake 9.0 i586 system. First, let me say that I can complile and install EMBOSS with no problems on this system. However, repeated attempts to install Jemboss have failed. One thing that is not very clear to me in the Jemboss intallation is the exact meaning of some of the setup prompts; I'm concerned that I may not be answering these prompts correctly and, cosequently, be causing the installation to fail. For instance, what is the meaning of "Enter java (1.3 or above) location [/usr]"? There is a "java" directory in /usr and it contains links to a jre-1.3.1_04 directory in /usr/lib. So, is it correct for me to accept the default answer /usr? Likewise, what is the meanining of "Enter EMBOSS download directory"? Does this refer to the EMBOSS-2.6.0 directory that is created by extracting the EMBOSS-2.6.0.tar file or to the directory above it? Finally, what is the best answer to "Enter where EMBOSS should be installed [/usr/local/emboss]"? In my case, the EMBOSS-2.6.0.tar file was extracted in /usr/local/emboss. My recollection is that the straight EMBOSS installation puts EMBOSS in /usr/local and its subdirectories. Wouldn't that be best for the Jemboss/EMBOSS installation, also? I haven't been able to find an explanation of these points in the available documentation, and it doesn't appear that these questions have been raised on the list during the last year (which makes me suspect that these are silly/stupid/dumb/nitwit questions). Thanks for your help. Jerry Mullersman ===== Jerald E. Mullersman, MD, PhD Associate Professor Department of Pathology East Tennessee State University PO Box 70568 Johnson City, TN 37614 phone: (423) 439-6210 fax: (423) 439-8060 From fernan at iib.unsam.edu.ar Tue Mar 4 15:55:06 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Tue, 4 Mar 2003 17:55:06 -0300 Subject: error in tfm.c Message-ID: <20030304205506.GF2971@iib.unsam.edu.ar> Hi! I have already finished the FreeBSD EMBOSS-2.6.0 port. In FreeBSD, documentation installed by third-parties goes into /usr/local/share/doc, and thus I now have all EMBOSS docs in /usr/local/share/doc/EMBOSS. This is unlike the rest of the shared data installed by EMBOSS, which goes in /usr/local/share/EMBOSS Now, I'm seeing an error when running tfm: [fernan at pi] tfm emma Displays a program's help documentation manual EMBOSS An error in tfm.c at line 63: The documentation for program 'emma' was not found. This happens with any EMBOSS program, not just with emma. This can be fixed by moving the docs to /usr/local/share/EMBOSS/doc. (In my case I created a link: cd /usr/local/share/EMBOSS/doc ln -s ../doc/EMBOSS doc) It appears then that tfm has a hard-coded reference to PREFIX/share/EMBOSS/doc to look for docs. If i want to place the docs somewhere else, where do I change this? I am no C guru but it seems to me that line 63 is not the right place. Are there other places/commands where this path is hard-coded? Now to a more general issue: is it possible to add a --docdir=DIR option to configure? Seems that there are several options to fine tune installation dirs, but not this one. Of course, then tfm (and perhaps others) should honor docdir. Right now I have to change one line in several Makefile.in files under EMBOSS-2.6.0/doc/ (using sed) to install docs in a place other than PREFIX/share/EMBOSS/doc. Though it works, it is certainly a hack (as the tfm error shows) and can be certainly managed more wisely if it can be set at configure time. Any thoughts? Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From tcarver at hgmp.mrc.ac.uk Tue Mar 4 16:03:55 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Tue, 4 Mar 2003 21:03:55 +0000 (GMT) Subject: installation of Jemboss from EMBOSS-2.6.0 package questions In-Reply-To: <20030304194338.74089.qmail@web11606.mail.yahoo.com> Message-ID: Hi Jerry, > "Enter java (1.3 or above) location [/usr]"? There is a "java" directory in > /usr and it contains links to a jre-1.3.1_04 directory in /usr/lib. So, is it > correct for me to accept the default answer /usr? I suspect you have in your path a /usr/bin/java which the script is picking up. If you type 'which java' it should tell you. I would recommend though that you get the latest J2SE 1.4.1 SDK though. > Likewise, what is the meanining of "Enter EMBOSS download directory"? This is the EMBOSS-2.6.0 directory location. It should give you this as the default in the square brackets. > Finally, what is the best answer to "Enter where > EMBOSS should be installed [/usr/local/emboss]"? In my case, the > EMBOSS-2.6.0.tar file was extracted in /usr/local/emboss. My recollection is > that the straight EMBOSS installation puts EMBOSS in /usr/local and its > subdirectories. Wouldn't that be best for the Jemboss/EMBOSS installation, > also? This is totally up to you where you want install to. I think people tend to use /usr/local/emboss if they want to keep emboss installation completely separate. Finally I would recommend a fresh download of all components (EMBOSS-2.6.0, Axis, and tomcat) when doing the installation. I hope this helps. Regards Tim Carver HGMP-RC From bioinfo at mascon.co.in Wed Mar 5 06:14:32 2003 From: bioinfo at mascon.co.in (bioinfo) Date: Wed, 5 Mar 2003 16:44:32 +0530 Subject: query Message-ID: <000801c2e308$6ddc68c0$63c809c0@bio> I need to find out if there is any module in emboss which does docking. I need to dock a fragment of a lead molecule into the active site of the target. I need to automate the whole process because i want to use the docked fragment as a startting material for generating ligands. Please tell me if there is some module that does docking so that i can incorporate it in my code. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030305/ce65df79/attachment.html From pmr at ebi.ac.uk Wed Mar 5 06:12:41 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 05 Mar 2003 11:12:41 +0000 Subject: error in tfm.c References: <20030304205506.GF2971@iib.unsam.edu.ar> Message-ID: <3E65DBA9.5070603@ebi.ac.uk> Fernan Aguero wrote: > It appears then that tfm has a hard-coded reference to > PREFIX/share/EMBOSS/doc to look for docs. If i want to place > the docs somewhere else, where do I change this? A simple fix is to add an EMBOSS_DOCROOT variable to emboss.default I will add this for the next release. > Now to a more general issue: is it possible to add a > --docdir=DIR option to configure? Seems that there are > several options to fine tune installation dirs, but not this > one. > > Of course, then tfm (and perhaps others) should honor > docdir. If possible, we could set this as the default value. Hope this helps, Peter From jison at hgmp.mrc.ac.uk Wed Mar 5 07:03:14 2003 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Wed, 05 Mar 2003 12:03:14 +0000 Subject: query References: <000801c2e308$6ddc68c0$63c809c0@bio> Message-ID: <3E65E782.D707D2B2@hgmp.mrc.ac.uk> No, there isn't. bioinfo wrote: > I need to find out if there is any module in emboss which does > docking. I need to dock a fragment of a lead molecule into the active > site of the target. I need to automate the whole process because i > want to use the docked fragment as a startting material for generating > ligands. Please tell me if there is some module that does docking so > that i can incorporate it in my code. -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ CCP11 : http://www.hgmp.mrc.ac.uk/CCP11/ From stefanielager at fastmail.ca Wed Mar 5 09:19:46 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Wed, 5 Mar 2003 09:19:46 -0500 (EST) Subject: LINDNA Message-ID: <3E660782.00007F.82648@ns.interchange.ca> It is possible to use the EMBOSS program restrict (for positions of restriction sites), if you parse the output. Genbank and EMBL entries can probably also be parsed (using perl). But lindna (and cirdna) aren't really worth the effort, they don't produce nice graphics either. There are several plasmiddrawing programs that can draw linear maps. Stefanie > Hi, > > I was looking at the lindna program, is there a program that can > create the input files needed for this from a genbank or embl > record? I saw the format needed for input, but couldn't find the > program to create a file in that format, I thought seqret might do > it? > > Thanks, _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From ame at esbs.u-strasbg.fr Wed Mar 5 10:44:25 2003 From: ame at esbs.u-strasbg.fr (Jean-Christophe AME) Date: Wed, 5 Mar 2003 16:44:25 +0100 Subject: Mutiple alignement of blast results Message-ID: <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> Hi all, I am looking for a program (preferably for unix or Mac) that does a multiple alignment of a blast result. There used to be Mulblast (http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it doesn't seem to work anymore with the last blast outputs. Does anybody have any idea on the subject. This could be a nice and useful EMBOSS program. Thanks for any help. Jean-Christophe ________________________ Jean-Christophe Am?, PhD U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et Structurale ?cole Sup?rieure de Biotechnologie de Strasbourg P?le API Boulevard S?bastien-Brant 67400 Illkirch France tel.: 33 3 90 24 47 05 Fax.: 33 3 90 24 46 86 http://parplink.u-strasbg.fr http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 920 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20030305/8088fd6f/attachment.bin From lmullan at hgmp.mrc.ac.uk Wed Mar 5 10:46:33 2003 From: lmullan at hgmp.mrc.ac.uk (Lisa Mullan) Date: Wed, 5 Mar 2003 15:46:33 -0000 Subject: Mutiple alignement of blast results In-Reply-To: <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> Message-ID: You could try putting your BLAST results into http://abs.cit.nih.gov/blast/ which will covert them to fasta format, and then you can carry on with your multiple sequence alignment. Discussions abound as to who might write a BLAST wrapper or EMBOSS, but nothing has happened so far, although there are offers! HTH Lisa Mullan -----Original Message----- From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk]On Behalf Of Jean-Christophe AME Sent: Wednesday, March 05, 2003 3:44 PM To: emboss at hgmp.mrc.ac.uk Subject: Mutiple alignement of blast results Hi all, I am looking for a program (preferably for unix or Mac) that does a multiple alignment of a blast result. There used to be Mulblast (http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it doesn't seem to work anymore with the last blast outputs. Does anybody have any idea on the subject. This could be a nice and useful EMBOSS program. Thanks for any help. Jean-Christophe ________________________ Jean-Christophe Am?, PhD U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et Structurale ?cole Sup?rieure de Biotechnologie de Strasbourg P?le API Boulevard S?bastien-Brant 67400 Illkirch France tel.: 33 3 90 24 47 05 Fax.: 33 3 90 24 46 86 http://parplink.u-strasbg.fr http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030305/f1b47221/attachment.html From fernan at iib.unsam.edu.ar Wed Mar 5 11:44:10 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Wed, 5 Mar 2003 13:44:10 -0300 Subject: Mutiple alignement of blast results In-Reply-To: <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> References: <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> Message-ID: <20030305164410.GE12578@iib.unsam.edu.ar> +----[ Jean-Christophe AME (05.Mar.2003 12:50): | | Hi all, | I am looking for a program (preferably for unix or Mac) that does a | multiple alignment of a blast result. There used to be Mulblast | (http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it | doesn't seem to work anymore with the last blast outputs. | +----] This is exactly what blixem does: Blixem - display Blast matches as a multiple alignment. Reference: Sonnhammer ELL & Durbin R (1994). A workbench for Large Scale Sequence Homology Analysis. Comput. Applic. Biosci. 10:301-307. http://www.cgr.ki.se/cgr/groups/sonnhammer/Blixem.html Hope this helps, Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From maltsev at mcs.anl.gov Wed Mar 5 13:00:43 2003 From: maltsev at mcs.anl.gov (Natalia Maltsev) Date: Wed, 05 Mar 2003 12:00:43 -0600 Subject: Mutiple alignement of blast results In-Reply-To: References: <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> Message-ID: <5.0.2.1.0.20030305112309.0389a008@mail.mcs.anl.gov> >Hi, You can try to use our new experimental server of BlocksBlast and Phyloblocks written by our Luke Ulrich. 1. BlocksBlast: http://compbio.mcs.anl.gov/blast/psiblast_phylo.html After you'll Blast your sequence you are given an option to select sequences and submit them to Phyloblocks directly from Blast (a standalone server for PhyloBlocks is at : http://compbio.mcs.anl.gov/ulrich/phyloblock/) It will allign the sequences using Clustalw and also give you a tree from which you can create the subsets using color coding of the clustal tree. You can send selected sequence groups to BlockMaker (Henikoff's ) to create HMM profiles, concensus sequences and alignments specific to the subsets. We will very much appreciate your comments about these tools. A paper describing these tools should be out shortly Cheers, Natalia Maltsev >-----Original Message----- >From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk]On >Behalf Of Jean-Christophe AME >Sent: Wednesday, March 05, 2003 3:44 PM >To: emboss at hgmp.mrc.ac.uk >Subject: Mutiple alignement of blast results > >Hi all, >I am looking for a program (preferably for unix or Mac) that does a >multiple alignment of a blast result. There used to be Mulblast >(http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it >doesn't seem to work anymore with the last blast outputs. > >Does anybody have any idea on the subject. This could be a nice and useful >EMBOSS program. >Thanks for any help. >Jean-Christophe > > > > > >________________________ >Jean-Christophe Am?, PhD >U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et Structurale >?cole Sup?rieure de Biotechnologie de Strasbourg >P?le API >Boulevard S?bastien-Brant >67400 Illkirch >France > >tel.: 33 3 90 24 47 05 >Fax.: 33 3 90 24 46 86 > >http://parplink.u-strasbg.fr >1A1A,1A1A,FFFF>http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html Natalia Maltsev Computational Biology Group Mathematics & Computer Science Division Argonne National Laboratory 9700 S. Cass Avenue Argonne, Illinois 60439 tel. (630) 252-5195 (of.) fax (630) 252-5986 E-mail: maltsev at mcs.anl.gov From georg.otto at tuebingen.mpg.de Wed Mar 5 13:49:41 2003 From: georg.otto at tuebingen.mpg.de (Georg Wilhelm Otto) Date: Wed, 5 Mar 2003 19:49:41 +0100 Subject: Mutiple alignement of blast results In-Reply-To: <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> Message-ID: <3959213E-4F3B-11D7-A36B-003065C99468@tuebingen.mpg.de> Hi Jean-Christoph, I usually do this in two steps: First i filter and align my blast results using MSPcrunch (see http://www.cgr.ki.se/cgr/groups/sonnhammer/MSPcrunch.html), then i visualize the result using BLIXEM (see http://www.cgr.ki.se/cgr/groups/sonnhammer/Blixem.html). hope that helps, georg On Wednesday, March 5, 2003, at 04:44 PM, Jean-Christophe AME wrote: > Hi all, > I am looking for a program (preferably for unix or Mac) that does a > multiple alignment of a blast result. There used to be Mulblast > (http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it > doesn't seem to work anymore with the last blast outputs. > > Does anybody have any idea on the subject. This could be a nice and > useful EMBOSS program. > Thanks for any help. > Jean-Christophe > > > > ________________________ > Jean-Christophe Am?, PhD > U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et > Structurale > ?cole Sup?rieure de Biotechnologie de Strasbourg > P?le API > Boulevard S?bastien-Brant > 67400 Illkirch > France > > tel.: 33 3 90 24 47 05 > Fax.: 33 3 90 24 46 86 > > http://parplink.u-strasbg.fr > http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1322 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20030305/26415074/attachment.bin From georg.otto at tuebingen.mpg.de Wed Mar 5 14:04:10 2003 From: georg.otto at tuebingen.mpg.de (Georg Wilhelm Otto) Date: Wed, 5 Mar 2003 20:04:10 +0100 Subject: Primer design Message-ID: <3F14B12D-4F3D-11D7-A36B-003065C99468@tuebingen.mpg.de> Hi all! I have a problem concerning PCR primer design. I have a lot of sequences of very different length and I want to design PCR primers to all of them within a given maximum distance from the 3-prime end - say 500 bp. I don't want to have to look at all the sequences because it is a lot. Primer3 does not seem to support this, it lets you only define ranges from the 5-prime end. Does anyone know how it could be done in Primer3 or how it could be done using another primer design software? Of course there is the obvious solution to revert the sequences and then define the distance from the 5-prime end, but i don't want to do this. Thanks a lot! Georg -- Georg Wilhelm Otto Max-Planck-Institute for Developmental Biology Spemannstrasse 35/III D-72076 Tuebingen Germany phone: +49 7071 601 301 http://www.eb.tuebingen.mpg.de From yezq at mail.cbi.pku.edu.cn Thu Mar 6 04:32:55 2003 From: yezq at mail.cbi.pku.edu.cn (Zhiqiang Ye) Date: Thu, 6 Mar 2003 17:32:55 +0800 Subject: single program complilaiton Message-ID: <200303060906.h2696Jj23619@mail.cbi.pku.edu.cn> Dear Sir/Madam?? I want to use only one(e.g. needle) or just several programs in EMBOSS package. Can I just compile these several programs , not the whole EMBOSS package? Thanks in advance! ???????????????? Best Regards! ????????????????????????????Zhiqiang Ye ??????????????????????????????????2003-03-06 From letondal at pasteur.fr Thu Mar 6 09:16:48 2003 From: letondal at pasteur.fr (Catherine Letondal) Date: Thu, 06 Mar 2003 15:16:48 +0100 Subject: Mutiple alignement of blast results In-Reply-To: Your message of "Wed, 05 Mar 2003 16:44:25 +0100." <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> Message-ID: <200303061416.h26EGnDS435024@electre.pasteur.fr> Jean-Christophe AME wrote: > Hi all, > I am looking for a program (preferably for unix or Mac) that does a=20 > multiple alignment of a blast result. There used to be Mulblast=20 > (http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it=20 > doesn't seem to work anymore with the last blast outputs. > > Does anybody have any idea on the subject. This could be a nice and=20 > useful EMBOSS program. > Thanks for any help. > Jean-Christophe > Hi Jean-Christophe, Just in case you don't have enough tools suggestion... : See, at: http://bioweb.pasteur.fr/seqanal/blast/intro-uk.html Blast post-processing: MSPcrunch MVIEW html4blast seqsblast (extraction of sequences from a Blast output) (alignment, then phylogenetic tools are then available on extracted sequences) -- Catherine Letondal -- Pasteur Institute Computing Center From rls at ebi.ac.uk Thu Mar 6 09:41:05 2003 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Thu, 6 Mar 2003 14:41:05 -0000 Subject: Mutiple alignement of blast results In-Reply-To: <200303061416.h26EGnDS435024@electre.pasteur.fr> Message-ID: Hi, Also, please take into consideration dbclustal which does what you need. You can see it working oif you run a wu-blast at the EBI against swall. Once the job is completed, click on Run dbclustal and choose which matches you wish to align. The reference to dbclustal is: "Rapid and reliable global multiple alignments of protein sequences detected by database searches" Thompson J.D., Plewnial F., Thierry J.-C. and Poch O. Nucleic Acid Research, 2000, Vol.28, No 15 2919-2926 R:) > -----Original Message----- > From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk]On > Behalf Of Catherine Letondal > Sent: 06 March 2003 14:17 > To: Jean-Christophe AME > Cc: emboss at hgmp.mrc.ac.uk > Subject: Re: Mutiple alignement of blast results > > > > Jean-Christophe AME wrote: > > Hi all, > > I am looking for a program (preferably for unix or Mac) that does a=20 > > multiple alignment of a blast result. There used to be Mulblast=20 > > (http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it=20 > > doesn't seem to work anymore with the last blast outputs. > > > > Does anybody have any idea on the subject. This could be a nice and=20 > > useful EMBOSS program. > > Thanks for any help. > > Jean-Christophe > > > > Hi Jean-Christophe, > > Just in case you don't have enough tools suggestion... : > See, at: http://bioweb.pasteur.fr/seqanal/blast/intro-uk.html > Blast post-processing: > MSPcrunch > MVIEW > html4blast > seqsblast (extraction of sequences from a Blast output) > (alignment, then phylogenetic tools are then > available on extracted > sequences) > > -- > Catherine Letondal -- Pasteur Institute Computing Center > From d.m.a.martin at dundee.ac.uk Thu Mar 6 09:57:21 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 06 Mar 2003 14:57:21 +0000 Subject: Getting database sizes for indexed databases Message-ID: Is there an easy way to determine the size (ie number of sequences) in a database? Could such information be added to showdb? I realise that in many cases this will be very difficult/impossible to determine. I am thinking of emblcd indexed databases. It must be possible to count the number of sequences in each file indexed and then use the file: wild cards to build a total for that database. regards ..d -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From pmr at ebi.ac.uk Thu Mar 6 10:13:18 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 06 Mar 2003 15:13:18 +0000 Subject: Getting database sizes for indexed databases References: Message-ID: <3E67658E.2080309@ebi.ac.uk> David Martin wrote: > Is there an easy way to determine the size (ie number of sequences) in a > database? > Could such information be added to showdb? > > I am thinking of emblcd indexed databases. It must be possible to count the > number of sequences in each file indexed and then use the file: wild cards > to build a total for that database. For EMBLCD databases it can be read from the index files (the number is in the header). For SRS databases a simple query can return the count. For complex cases there may be no answer - but we can either write a short message, or add an attribute to the database definition in emboss.default. So ... is this a useful addition to showdb? Peter From gwilliam at hgmp.mrc.ac.uk Thu Mar 6 10:22:09 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 06 Mar 2003 15:22:09 +0000 Subject: Getting database sizes for indexed databases References: <3E67658E.2080309@ebi.ac.uk> Message-ID: <3E6767A0.B906E106@hgmp.mrc.ac.uk> Or should it be reported by a seprarate program? Peter Rice wrote: > > So ... is this a useful addition to showdb? > > Peter -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From d.m.a.martin at dundee.ac.uk Thu Mar 6 10:24:34 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 06 Mar 2003 15:24:34 +0000 Subject: Getting database sizes for indexed databases In-Reply-To: <3E67658E.2080309@ebi.ac.uk> Message-ID: On 6/3/03 3:13 pm, "Peter Rice" wrote: > David Martin wrote: >> Is there an easy way to determine the size (ie number of sequences) in a >> database? >> Could such information be added to showdb? >> >> I am thinking of emblcd indexed databases. It must be possible to count the >> number of sequences in each file indexed and then use the file: wild cards >> to build a total for that database. > > For EMBLCD databases it can be read from the index files (the number is > in the header). It can if the database definition matches the files indexed. eg I have swiss, trembl and trembl_new all indexed together as sptr. I use the same index files for sw (swiss only) and trembl (trembl+trembl_new) The index file will give the total for all three or the total for each file? If it is the total for each file then the true count for subdivisions of the database can be found by matching the file: definition to the list of files int he header. If it is the global total then there is no direct way of determining the database size without specifically capturing that with the indexing program. What is the header format for the index files? ..d > > For SRS databases a simple query can return the count. > > For complex cases there may be no answer - but we can either write a > short message, or add an attribute to the database definition in > emboss.default. > > So ... is this a useful addition to showdb? > > Peter > > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From jrvalverde at cnb.uam.es Thu Mar 6 10:44:44 2003 From: jrvalverde at cnb.uam.es (José R. Valverde) Date: Thu, 6 Mar 2003 16:44:44 +0100 Subject: Getting database sizes for indexed databases In-Reply-To: References: Message-ID: <20030306164444.537c8216.jrvalverde@cnb.uam.es> On Thu, 06 Mar 2003 14:57:21 +0000 David Martin wrote: > > Is there an easy way to determine the size (ie number of sequences) in a > database? > Could such information be added to showdb? > The easy way: grep $entry database May not give you what you want if you refer not to records but entry numbers. Ah, but then this happens in databases like embl and swissprot.. The even easier way: See the README file which contains the number of entries. j From d.m.a.martin at dundee.ac.uk Thu Mar 6 12:04:55 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 06 Mar 2003 17:04:55 +0000 Subject: problems with indexing refseq Message-ID: I am getting strange behaviour with refseq. When indexing the genbank format cumulative files (rscu.gbff) with dbiflat -idformat GB I get an index that returns the wrong sequences. eg attempting to retrieve NM_060207 instead retrieves NM_131801 which is a totally different sequence entry. Attempting to retrieve NM131801 gives NM_165909. Any thoughts on how to debug this effect. entret -debug indicates that the right entry is found in the index but the entry read is incorrect. ..d -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From squiresb at macrogenics.com Tue Mar 11 23:03:54 2003 From: squiresb at macrogenics.com (Burke Squires) Date: Tue, 11 Mar 2003 22:03:54 -0600 Subject: I have an accession number, can I extract genbank information from an on-line database? Message-ID: Hello EMBOSSers, Is it possible to extract genbank file information from an on-line database if I have an accession number or do I have to download the hundreds of genbank files locally and extract it from that? If so how? I have read information on seqret and it seems truly wonderful but it seems to work only with local databases? Thanks! Burke Squires -- Burke Squires Bioinformatics MacroGenics, Inc. Dallas, TX From David.Bauer at SCHERING.DE Wed Mar 12 01:42:30 2003 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Wed, 12 Mar 2003 07:42:30 +0100 Subject: I have an accession number, can I extract genbank information from an on-line database? Message-ID: (See attached file: C.htm) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030312/cfd319a3/attachment.htm From hkawai at venus.dti.ne.jp Wed Mar 12 06:13:13 2003 From: hkawai at venus.dti.ne.jp (Hironori Kawai) Date: Wed, 12 Mar 2003 20:13:13 +0900 Subject: problems with indexing refseq In-Reply-To: References: Message-ID: <200303121111.h2CBBrME027328@smtp4.dti.ne.jp> Hello David Martin wrote: > I am getting strange behaviour with refseq. > > When indexing the genbank format cumulative files (rscu.gbff) with dbiflat > -idformat GB I get an index that returns the wrong sequences. > > eg attempting to retrieve NM_060207 instead retrieves NM_131801 which is a > totally different sequence entry. > Attempting to retrieve NM131801 gives NM_165909. This problem was described in this ML. If you are using version 2.5.0 or earlier (I guess you do so), I recommend to update this to 2.5.1 or later. In addition, you have to reformat rscu.gbff file in the way that the word following LOCUS in each entry is replaced to their Accession No. In this ML, a perl script which reformats in such way, are uploaded (the Message-ID <2DC41140A89ED411989D00508BDCD9ED01E28754@ bi-exsrv1.iapc.bbsrc.ac.uk>). Hironori Kawai From siegmund at develogen.com Wed Mar 12 06:28:25 2003 From: siegmund at develogen.com (Thomas Siegmund) Date: Wed, 12 Mar 2003 12:28:25 +0100 Subject: I have an accession number, can I extract genbank information from an on-line database? In-Reply-To: References: Message-ID: <200303121228.25817.siegmund@develogen.com> Hi Burke, if you have blast databases in house, you can use fastacmd (comes with blast) to extract single sequences in fasta format from the binary database. With a emboss.default like this you can access the blast database in EMBOSS: DB nt [ methodentry: app app: "fastacmd -d/data/blast/data/nt -s%s" type: N format: fasta comment: "nt - non redundant nucleotide sequences" ] Regards Thomas Am Mittwoch, 12. M?rz 2003 05:03 schrieb Burke Squires: > Hello EMBOSSers, > > Is it possible to extract genbank file information from an on-line database > if I have an accession number or do I have to download the hundreds of > genbank files locally and extract it from that? If so how? I have read > information on seqret and it seems truly wonderful but it seems to work > only with local databases? > > Thanks! > > Burke Squires -- Thomas Siegmund, Ph.D. DeveloGen AG Bioinformatics and Data Management Phone: +49(551) 505 58 651 From jison at hgmp.mrc.ac.uk Wed Mar 12 08:42:37 2003 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Wed, 12 Mar 2003 13:42:37 +0000 Subject: EMBOSS Programming Course Message-ID: <3E6F394D.E4C4830B@hgmp.mrc.ac.uk> Hi Details on a forthcoming FREE programming course for bioinformatics using EMBOSS are below. Apologies if not interested. Please forward to anyone you think might be interested. Cheers Jon Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk BSDC 2003 Bioinformatics Software Development Courses May 13-15, June 17-19, Sep 16-18 2003 A course on 'Bioinformatics Software Development' using EMBOSS will be held in the training room at Hinxton Hall on May 13-15, June 17-19 and Sep 16-18 2003. The course will give a good introduction to programming in EMBOSS. By the end of the course you will be experienced in all the steps in writing a basic bioinformatics application using the EMBOSS programming libraries. The course would suit competent programmers, probably with at least a couple of years of experience. A reasonable working knowledge of C is required, familiarity with pointers is helpful but not essential. The three dates are likely to get booked up very quickly so please email Karen Hampson (khampson at hgmp.mrc.ac.uk) to register as soon as possible. To read more about EMBOSS see EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ From Johanne.Duhaime at ircm.qc.ca Wed Mar 12 16:29:17 2003 From: Johanne.Duhaime at ircm.qc.ca (Duhaime Johanne) Date: Wed, 12 Mar 2003 16:29:17 -0500 Subject: Seqret does not work in a crontab Message-ID: <75CDD43E62D698448ED86E23C290A2760A2B90@pandore.ircm.priv> Hello I have a perl program that use "seqret" to retrieve a list of sequences (and do other things). The target command used is: seqret -sequence=@/seqdata/seqdatabases/protein_embl/mammalian/mammalian.id -outseq=/seqdata/seqdatabases/protein_embl/mammalian/mammalian.dat -osformat=SWISS The file /seqdata/seqdatabases/protein_embl/mammalian/mammalian.id contains names of sequenes like: prot:143B_BOVIN prot:143B_HUMAN prot:143B_MOUSE (...) and prot is define in .embossrc This program works fine on the command line call. The problem arises when I put that program in a crontab. Then I have the following: Reads and writes (returns) sequences Error: failed to open filename prot Error: Unable to read sequence '@/seqdata/seqdatabases/protein_embl/mammalian/mammalian.id' erreur : It looks like it could recognize "prot". Can you help me? From squiresb at macrogenics.com Wed Mar 12 20:43:49 2003 From: squiresb at macrogenics.com (Burke Squires) Date: Wed, 12 Mar 2003 19:43:49 -0600 Subject: Accessing online databases... In-Reply-To: Message-ID: Hello, Thanks for your help! If I could ask another questions...I checked out the admin?s guide and I found the following information: DB mydb [ # required parameters method: url format: genbank url: "http://www.infobiogen.fr/srs5bin/cgi-bin/wgetz?-e+[genbank-id:%s]" #optional parameters type: N comment: "Genbank by ID from InfoBiogen" ] I have also found and pasted this into my emboss.default.template. What do I need to do to get this to show up in ?showdb?? Any information or URL?s to accessing an online database using a Genbank accession number would be greatly appreciated! Thanks! Burke -- Burke Squires Bioinformatics MacroGenics, Inc. 2600 Stemmons Freeway, Suite 210 Dallas, TX 75235 USA Work: 214-634-3000 X224 Fax: 214-634-3002 ---------------------------------------------------------------------------- This e-mail and any attachments may be confidential or legally privileged. If you received this message in error or are not the intended recipient, you should destroy the e-mail message and any attachments or copies, and you are prohibited from retaining, distributing, disclosing or using any information contained herein. Please inform us of the erroneous delivery by return e-mail. Thank you for your cooperation. > > From: David.Bauer at SCHERING.DE > Date: Wed, 12 Mar 2003 07:42:30 +0100 > To: squiresb at macrogenics.com > Cc: emboss at embnet.org > Subject: Re: I have an accession number, can I extract genbank information > from an on-line database? > > > > (See attached file: C.htm) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030312/d70d1f41/attachment.html From ableasby at hgmp.mrc.ac.uk Thu Mar 13 05:31:09 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 13 Mar 2003 10:31:09 GMT Subject: Accessing online databases... Message-ID: <200303131031.h2DAV9V16580@bromine.hgmp.mrc.ac.uk> Burke, You need to rename emboss.default.template to emboss.default. The URL given in the admin guide is out of date. You'll have to replace your entry with something like: DB mydb [ # required parameters method: url format: genbank url: "http://www.infobiogen.fr/srs7bin/cgi-bin/wgetz?-e+-ascii+[genbank-id:%s]" #optional parameters type: N comment: "Genbank by ID from InfoBiogen" ] HTH Alan Bleasby HGMP From Wiepert.Mathieu at mayo.edu Thu Mar 13 07:57:25 2003 From: Wiepert.Mathieu at mayo.edu (Wiepert, Mathieu) Date: Thu, 13 Mar 2003 06:57:25 -0600 Subject: est2genome output to genbank format? Message-ID: <2F41CC6C9777D311ACBD009027B108EA0541C558@excsrv32.mayo.edu> Hi, Is it possible to have est2genome give output in genbank format (or ensembl), with exons and introns annotated as features on the genome sequence? OR is there something that can take the output and parse it into that format? Description of the tool notes that " This format is easy to parse into other software. " wondered if someone had come up with a handy widget to do something like this, or if it was already available. Thanks, -Mat From jason at cgt.mc.duke.edu Thu Mar 13 09:00:50 2003 From: jason at cgt.mc.duke.edu (Jason Stajich) Date: Thu, 13 Mar 2003 09:00:50 -0500 (EST) Subject: est2genome output to genbank format? In-Reply-To: <2F41CC6C9777D311ACBD009027B108EA0541C558@excsrv32.mayo.edu> References: <2F41CC6C9777D311ACBD009027B108EA0541C558@excsrv32.mayo.edu> Message-ID: Mat - Bio::Tools::Est2Genome ... Although it doesn't construct proper genes as I would like. -jason On Thu, 13 Mar 2003, Wiepert, Mathieu wrote: > Hi, > > Is it possible to have est2genome give output in genbank format (or ensembl), with exons and introns annotated as features on the genome sequence? OR is there something that can take the output and parse it into that format? Description of the tool notes that " This format is easy to parse into other software. " wondered if someone had come up with a handy widget to do something like this, or if it was already available. > > Thanks, > > -Mat > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From pmr at ebi.ac.uk Thu Mar 13 09:14:54 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 13 Mar 2003 14:14:54 +0000 Subject: est2genome output to genbank format? References: <2F41CC6C9777D311ACBD009027B108EA0541C558@excsrv32.mayo.edu> Message-ID: <3E70925E.9080009@ebi.ac.uk> Wiepert, Mathieu wrote: > Is it possible to have est2genome give output in genbank format (or ensembl), > with exons and introns annotated as features on the genome sequence? Soon ... EMBOSS reports can be written as GFF or EMBL feature tables. All you need is a change to est2genome to write an EMBOSS report. The main reason est2genome has not been converted yet is the need to also write an alignment report and to preserve the original format for users who already parse it into something else. High on the list of things to do ... especially now someone has asked for it :-) Expect something in the next couple of months. As for other parsers for est2genome .... there are parsers at the Sanger Institute for their annotation pipelines. You could try contacting them for help and advice. regards, Peter Rice From battaile at mcw.edu Thu Mar 13 10:33:23 2003 From: battaile at mcw.edu (Kevin Battaile) Date: Thu, 13 Mar 2003 09:33:23 -0600 (CST) Subject: jemboss installation question Message-ID: <38634.141.106.116.74.1047569603.squirrel@post.its.mcw.edu> I have been trying to install jemboss in client-server mode on a redhat linux box (7.3 and 8.0) without much success. I can get the standalone version working on the 8.0 box (haven't tried on the 7.3 box) but the trouble seems to start when I want to go client-server. I have the following distributions: EMBOSS-2.6.0 j2sdk1.4.0_01 jakarta-tomcat-4.0.4 xml-axis-10 I run the install-jemboss-server.sh script as myself, and I also own the jakarta and xml-axis directories. Everything seems to go fine during the installation. Tomstart appears to start tomcat as I can get the tomcat web page saying it is installed. When I run runJemboss.csh, I get a bunch of error messages spewing out on the terminal window. I login using my linux username and password and when I try to run anything I get a window that says there is a problem connecting to the server. I pasted a portion of the error messages below. Does anyone have any idea what I could be doing wrong? I like the standalone interface and would like to get the client-server version working so the people in our group can use it from their pc. Thanks, Kevin ======================================= [battaile at linux3 jemboss]$ ./runJemboss.csh [1] 4093 [battaile at linux3 jemboss]$ Warning: Cannot convert string "Escape,_Key_Cancel" to type VirtualBinding Warning: Cannot convert string "Home,_Key_Begin" to type VirtualBinding Warning: Cannot convert string "F1,_Key_Help" to type VirtualBinding Warning: Cannot convert string "ShiftF10,_Key_Menu" to type VirtualBinding Warning: Cannot convert string "F10,Shift_Key_Menu" to type VirtualBinding Warning: Cannot convert string "KP_Enter,_Key_Execute" to type VirtualBinding Warning: Cannot convert string "AltReturn,Alt_Key_KP_Enter" to type VirtualBinding calling the server Mar 13, 2003 9:16:57 AM org.apache.axis.client.Call invoke INFO: Mapping Exception to AxisFault AxisFault faultCode: {http://xml.apache.org/axis/}Server.userException faultString: java.lang.NullPointerException faultActor: null faultDetail: stackTrace: java.lang.NullPointerException at org.emboss.jemboss.programs.RunEmbossApplication.isProcessStdout(RunEmbossApplication.java:71) at org.emboss.jemboss.server.JembossAuthServer.show_db(JembossAuthServer.java:326) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:324) at org.apache.axis.providers.java.RPCProvider.invokeMethod(RPCProvider.java:372) at org.apache.axis.providers.java.RPCProvider.processMessage(RPCProvider.java:292) at org.apache.axis.providers.java.JavaProvider.invoke(JavaProvider.java:276) at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:71) at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:156) at org.apache.axis.SimpleChain.invoke(SimpleChain.java:126) at org.apache.axis.handlers.soap.SOAPService.invoke(SOAPService.java:437) at org.apache.axis.server.AxisServer.invoke(AxisServer.java:316) at org.apache.axis.transport.http.AxisServlet.doPost(AxisServlet.java:701) at javax.servlet.http.HttpServlet.service(HttpServlet.java:760) at org.apache.axis.transport.http.AxisServletBase.service(AxisServletBase.java:335) at javax.servlet.http.HttpServlet.service(HttpServlet.java:853) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:247) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:243) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:190) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566) at org.apache.catalina.valves.CertificatesValve.invoke(CertificatesValve.java:246) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943) at org.apache.catalina.core.StandardContext.invoke(StandardContext.java:2347) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:180) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566) at org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherValve.java:170) From david at cnb.uam.es Thu Mar 13 11:10:06 2003 From: david at cnb.uam.es (David Garcia Aristegui) Date: Thu, 13 Mar 2003 17:10:06 +0100 Subject: jemboss installation question In-Reply-To: <38634.141.106.116.74.1047569603.squirrel@post.its.mcw.edu> References: <38634.141.106.116.74.1047569603.squirrel@post.its.mcw.edu> Message-ID: Don?t worry about the firsts warnings ( is a common problem with the java interface an the Red Hat, for example ). About the java errors: it seems you have a problem with the Tomcat or the Axis/SOAP installation. - Tomcat is runnig for sure? you can execute properly the examples from your own tomcat installation? - Look at the catalina.out logs under the tomcat installation, it gives you lot of information; look what is the port reserved for tomcat, other process are runnig on the same port?. - If you have to run again the install script: check out the java environment variable. - Install script: "The script asks for the locations of the EMBOSS download, EMBOSS installation, Tomcat, Axis and Java directories. Axis is added to the Tomcat (copying soap.war to $TOMCAT/webapps/ )." Copy the soap.war again... and restart. "The Jemboss server classes are added to the Tomcat CLASSPATH ($TOMCAT/webapps/axis/WEB-INF/classes/)". Look at the classes directory, and check the symbolic links, they are pointing the correct files? Maybe is a path problem. - Check out the jemboss.properties file under $EMBOSS_ROOT/share/EMBOSS/jemboss/resource/jemboss.properties. Hope this helps, and excuse me, my english is terrible. David. >I have been trying to install jemboss in client-server mode on a redhat >linux box (7.3 and 8.0) without much success. I can get the standalone >version working on the 8.0 box (haven't tried on the 7.3 box) but the >trouble seems to start when I want to go client-server. > >I have the following distributions: >EMBOSS-2.6.0 >j2sdk1.4.0_01 >jakarta-tomcat-4.0.4 >xml-axis-10 > >I run the install-jemboss-server.sh script as myself, and I also own the >jakarta and xml-axis directories. Everything seems to go fine during the >installation. Tomstart appears to start tomcat as I can get the tomcat web >page saying it is installed. When I run runJemboss.csh, I get a bunch of >error messages spewing out on the terminal window. I login using my linux >username and password and when I try to run anything I get a window that >says there is a problem connecting to the server. I pasted a portion of >the error messages below. > >Does anyone have any idea what I could be doing wrong? I like the >standalone interface and would like to get the client-server version >working so the people in our group can use it from their pc. > >Thanks, > >Kevin > >======================================= > >[battaile at linux3 jemboss]$ ./runJemboss.csh >[1] 4093 >[battaile at linux3 jemboss]$ Warning: Cannot convert string >"Escape,_Key_Cancel" to type VirtualBinding >Warning: Cannot convert string "Home,_Key_Begin" to type VirtualBinding >Warning: Cannot convert string "F1,_Key_Help" to type VirtualBinding >Warning: Cannot convert string "ShiftF10,_Key_Menu" to type >VirtualBinding >Warning: Cannot convert string "F10,Shift_Key_Menu" to type >VirtualBinding >Warning: Cannot convert string "KP_Enter,_Key_Execute" to type >VirtualBinding >Warning: Cannot convert string "AltReturn,Alt_Key_KP_Enter" to type >VirtualBinding >calling the server >Mar 13, 2003 9:16:57 AM org.apache.axis.client.Call invoke >INFO: Mapping Exception to AxisFault >AxisFault > faultCode: {http://xml.apache.org/axis/}Server.userException > faultString: java.lang.NullPointerException > faultActor: null > faultDetail: > stackTrace: java.lang.NullPointerException > at >org.emboss.jemboss.programs.RunEmbossApplication.isProcessStdout(RunEmbossApplication.java:71) > at >org.emboss.jemboss.server.JembossAuthServer.show_db(JembossAuthServer.java:326) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at >sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at >sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:324) > at >org.apache.axis.providers.java.RPCProvider.invokeMethod(RPCProvider.java:372) > at >org.apache.axis.providers.java.RPCProvider.processMessage(RPCProvider.java:292) > at >org.apache.axis.providers.java.JavaProvider.invoke(JavaProvider.java:276) > at >org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:71) > at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:156) > at org.apache.axis.SimpleChain.invoke(SimpleChain.java:126) > at >org.apache.axis.handlers.soap.SOAPService.invoke(SOAPService.java:437) > at org.apache.axis.server.AxisServer.invoke(AxisServer.java:316) > at >org.apache.axis.transport.http.AxisServlet.doPost(AxisServlet.java:701) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:760) > at >org.apache.axis.transport.http.AxisServletBase.service(AxisServletBase.java:335) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:853) > at >org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:247) > at >org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:193) > at >org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:243) > at >org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566) > at >org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472) > at >org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943) > at >org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:190) > at >org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566) > at >org.apache.catalina.valves.CertificatesValve.invoke(CertificatesValve.java:246) > at >org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564) > at >org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472) > at >org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943) > at >org.apache.catalina.core.StandardContext.invoke(StandardContext.java:2347) > at >org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:180) > at >org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566) > at >org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherValve.java:170) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030313/1f15e180/attachment.html From Jack.Leunissen at wur.nl Thu Mar 13 17:54:54 2003 From: Jack.Leunissen at wur.nl (Jack Leunissen) Date: Thu, 13 Mar 2003 23:54:54 +0100 Subject: Accessing online databases... In-Reply-To: <200303131031.h2DAV9V16580@bromine.hgmp.mrc.ac.uk> Message-ID: <006701c2e9b3$904d2d70$0300000a@kuifje> Also note the change from SRS5 to SRS7. Version 5 is out of date by several years. I guess that manual needs some cleaning up... Cheers, Jack Jack A.M. Leunissen Genome Informatics Wageningen University 6703 HA Wageningen, NL > -----Original Message----- > From: owner-emboss at hgmp.mrc.ac.uk > [mailto:owner-emboss at hgmp.mrc.ac.uk] On Behalf Of > ableasby at hgmp.mrc.ac.uk > Sent: Thursday, 13 March, 2003 11:31 > To: emboss at hgmp.mrc.ac.uk; squiresb at macrogenics.com > Subject: Re: Accessing online databases... > > > Burke, > > You need to rename emboss.default.template to emboss.default. > > The URL given in the admin guide is out of date. You'll > have to replace your entry with something like: > > DB mydb [ > # required parameters > method: url > format: genbank > url: > "http://www.infobiogen.fr/srs7bin/cgi-bin/wgetz?-e+-ascii+[gen bank-id:%s]" #optional parameters type: N comment: "Genbank by ID from InfoBiogen" ] HTH Alan Bleasby HGMP From kellert at ohsu.edu Thu Mar 13 17:58:48 2003 From: kellert at ohsu.edu (Thomas Keller) Date: Thu, 13 Mar 2003 14:58:48 -0800 Subject: tempdata availability Message-ID: <59C9956D-55A7-11D7-AAF0-0003930405E2@ohsu.edu> Greetings, I must be missing something obvious. I know eprimer3 is working, I've used it with my own datafiles. But when I try to use the test databases I get the following: kellert% eprimer3 tembl:hsfau1 hsfau.eprimer3 -explain Picks PCR primers and hybridization oligos Warning: Cannot open division file '' for database 'tembl' Warning: seqCdQry failed Error: Unable to read sequence 'tembl:hsfau1' ########################### My embossdata output follows, but I thought emboss.default would be used to look in /my_emboss_path/EMBOSS/test for the test dbs. I have set my_emboss_path in emboss.defaults. kellert% embossdata Finds or fetches the data files read in by the EMBOSS programs # The following directories can contain EMBOSS data files. # They are searched in the following order until the file is found. # If the directory does not exist, then this is noted below. # '.' is the UNIX name for your current working directory. . Exists .embossdata Does not exist /Users/kellert Exists /Users/kellert/.embossdata Does not exist /usr/local/biotools/share/EMBOSS/data/ Exists ################# Thanks for your help, Tom Thomas J. Keller, Ph.D. Director, MMI Core Facility Oregon Health & Science University 3181 SW Sam Jackson Park Rd. Portland, OR, USA, 97239 http://www.ohsu.edu/core From d.m.a.martin at dundee.ac.uk Thu Mar 13 18:41:14 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 13 Mar 2003 23:41:14 +0000 Subject: Accessing online databases... In-Reply-To: <006701c2e9b3$904d2d70$0300000a@kuifje> Message-ID: On 13/3/03 10:54 pm, "Jack Leunissen" wrote: > Also note the change from SRS5 to SRS7. Version 5 is out of date > by several years. I guess that manual needs some cleaning up... There have been a lot of changes since I last updated it. Someone else had offered to update it with th elatest developments as I have not had the time. ..d > > Cheers, > Jack > > > > Jack A.M. Leunissen > Genome Informatics > Wageningen University > 6703 HA Wageningen, NL > > > >> -----Original Message----- >> From: owner-emboss at hgmp.mrc.ac.uk >> [mailto:owner-emboss at hgmp.mrc.ac.uk] On Behalf Of >> ableasby at hgmp.mrc.ac.uk >> Sent: Thursday, 13 March, 2003 11:31 >> To: emboss at hgmp.mrc.ac.uk; squiresb at macrogenics.com >> Subject: Re: Accessing online databases... >> >> >> Burke, >> >> You need to rename emboss.default.template to emboss.default. >> >> The URL given in the admin guide is out of date. You'll >> have to replace your entry with something like: >> >> DB mydb [ >> # required parameters >> method: url >> format: genbank >> url: >> "http://www.infobiogen.fr/srs7bin/cgi-bin/wgetz?-e+-ascii+[gen > bank-id:%s]" > #optional parameters > type: N > comment: "Genbank by ID from InfoBiogen" > ] > > > HTH > > Alan Bleasby > HGMP > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From Johanne.Duhaime at ircm.qc.ca Fri Mar 14 15:14:59 2003 From: Johanne.Duhaime at ircm.qc.ca (Duhaime Johanne) Date: Fri, 14 Mar 2003 15:14:59 -0500 Subject: TR: Seqret does not work in a crontab Message-ID: <75CDD43E62D698448ED86E23C290A2760A3783@pandore.ircm.priv> Thank you everyone for answers. The problem was solved by putting .embossrc in the $HOME of the user. ------ I have a perl program that use "seqret" to retrieve a list of sequences (and do other things). The target command used is: seqret -sequence=@/seqdata/seqdatabases/protein_embl/mammalian/mammalian.id -outseq=/seqdata/seqdatabases/protein_embl/mammalian/mammalian.dat -osformat=SWISS The file /seqdata/seqdatabases/protein_embl/mammalian/mammalian.id contains names of sequenes like: prot:143B_BOVIN prot:143B_HUMAN prot:143B_MOUSE (...) and prot is define in .embossrc This program works fine on the command line call. The problem arises when I put that program in a crontab. Then I have the following: Reads and writes (returns) sequences Error: failed to open filename prot Error: Unable to read sequence '@/seqdata/seqdatabases/protein_embl/mammalian/mammalian.id' erreur : It looks like it could recognize "prot". Can you help me? From davids at synpep.com Fri Mar 14 17:26:59 2003 From: davids at synpep.com (David Stephens) Date: Fri, 14 Mar 2003 14:26:59 -0800 Subject: How to Save Time, Resources and Expenses by Outsourcing Peptide Synthesis Message-ID: <20030314223432.4EE737D256@mercury.hgmp.mrc.ac.uk> An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030314/23d40ca6/attachment.html From tomembers at premiumsmail.net Sun Mar 16 04:39:23 2003 From: tomembers at premiumsmail.net (Reunion.com) Date: Sun, 16 Mar 2003 01:39:23 -0800 Subject: Is Your High School Sweetheart Single? Message-ID: <20030316094938.19CC17D0DE@mercury.hgmp.mrc.ac.uk> WHERE IS YOUR HIGH SCHOOL SWEETHEART NOW? Find out by joining Reunion.com today. Access your High School class list, emails, message boards and photos or find out if your old Prom Queen is still single! You never know what can happen when you reconnect with your past... http://www.premiumsmail.net/cgi-bin/st.cgi?cmp=486TA&cd=premium ************************************************************************ The preceding advertisement was sent you by virtue of your participation in the Special Product Offerings of PremiumsMail or our partners. To unsubscribe from receiving further emails from PremiumsMail's Special Product Offerings please click here: http://www.premiumsmail.net/cgi-bin/df.cgi?camp_id=486_41758636&client_d=premium&email_id=emboss at embnet.org We currently show the email that you have used to become a part of our mailing list as: emboss at embnet.org. For information about how PremiumsMail obtained your name and how PremiumsMail operates this list, please review our http://www.Premiumsmail.net/privacy.html As is stated in our Privacy Policy, PremiumsMail does not promote or endorse any of the companies advertising through us. Please contact PremiumsMail for any comments you may have regarding your participation. We may transfer your e-mail address to our partners at any time. *********************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030316/a911710c/attachment.html From xbizoy01 at yahoo.fr Mon Mar 17 03:22:55 2003 From: xbizoy01 at yahoo.fr (=?iso-8859-1?q?yann=20bizouerne?=) Date: Mon, 17 Mar 2003 09:22:55 +0100 (CET) Subject: Index EMBL and EMBLnew Message-ID: <20030317082255.68285.qmail@web20803.mail.yahoo.com> I want to work with EMBL and EMBLnew. I have index the EMBL files and the EMBL new filers in separate directories.(/EMBL/ & /EMBLnew/). I did this because I just want to re-index EMBLnew when new sequences are coming, and not all the sequences (EMBL + EMBLnew) Now I want to interogate againts these two databases with one request. How could I do such thing ? Is it the good way to work with EMBL or not ? Thanks in advance for your help. Yann BIZOUERNE --------------------------------- Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en fran?ais ! Testez le nouveau Yahoo! Mail -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030317/2c02e667/attachment.html From pmr at ebi.ac.uk Mon Mar 17 05:46:25 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 17 Mar 2003 10:46:25 +0000 Subject: Index EMBL and EMBLnew References: <20030317082255.68285.qmail@web20803.mail.yahoo.com> Message-ID: <3E75A781.4060708@ebi.ac.uk> yann bizouerne wrote: > I want to work with EMBL and EMBLnew. I have index the EMBL files and > the EMBL new filers in separate directories.(/EMBL/ & /EMBLnew/). > > I did this because I just want to re-index EMBLnew when new sequences > are coming, and not all the sequences (EMBL + EMBLnew) > > Now I want to interogate againts these two databases with one request. > How could I do such thing ? Is it the good way to work with EMBL or not ? This is my next EMBOSS task!!! You can of course already do this with SRS. If you put both databases together, EMBOSS will have problems with duplicate IDs. For now, the EMBOSS solution is to use "whichdb" which will search all your databases for an entry. If it reports an entry in EMBL and EMBLNEW you can use the EMBLNEW entry. I am planning to extend the EMBOSS "USA" syntax to include features of the SRS query language, including a query of more than one database, more than one field, and more than one text string (and of course ... more than one query) To query EMBL and EMBLNEW you also need to exclude matching entries - I can add that by excluding matching IDs from EMBL. I hope to do this by defining an "EMBLALL" database to make life easier for users. SWISSPROT/SWISSNEW/SPTREMBL is more difficult because the matches have to be by accession number. There is already a non-redundant "swall" database available so this is not such a high priority and may have to wait for a way to link databases in EMBOSS (but the internal EMBOSS code does allow for this kind of extension). Hope this helps, Peter Rice From gvasudevan at medarex.com Mon Mar 17 16:50:04 2003 From: gvasudevan at medarex.com (Vasudevan, Geetha) Date: Mon, 17 Mar 2003 13:50:04 -0800 Subject: hydropathicity... Message-ID: <8249C3256E593D4FB066BB9998D9F7E41CF157@ca2-fs03.ca2.2k.medarex.com> I am trying to calulate normalized consensus hydropathicity values for a given seq using PEPINFO. It uses Eaa_hyropathy.dat file which has Kyte-Doo indices, OHM and consensus values. Are the consensus ones same as normalized consensus scale (ref:Eisenberg D.; Schwarz E.; Komarony M.; Wall R. J. Mol. Biol. 1984, 179, 125-142) ? Thanks for any feedback. -Geetha. From Wiepert.Mathieu at mayo.edu Mon Mar 17 16:57:37 2003 From: Wiepert.Mathieu at mayo.edu (Wiepert, Mathieu) Date: Mon, 17 Mar 2003 15:57:37 -0600 Subject: specifying octanol output filename Message-ID: <2F41CC6C9777D311ACBD009027B108EA0541C59B@excsrv32.mayo.edu> Hi, Is there a way to redirect octanol output to a filename of my choosing? I looked through the Command line docs but couldn't find anything. I thought there was a global option like -output or -outfile, but I can't seem to get anything to work with octanol. All output is named octanol.1.png (used -graph png option). Simple enough to add a second line of code to rename the file, but seems different than the other programs I have used so far. While I am at it, I have one file with many sequences, in fasta format. Can octanol create output for all the sequences with one call? I can easily get around this as well, but many programs seem to take files with many sequences, thought I would ask. Thanks, -Mat From stefanielager at fastmail.ca Tue Mar 18 01:14:03 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Tue, 18 Mar 2003 01:14:03 -0500 (EST) Subject: specifying octanol output filename Message-ID: <3E76B92B.00015B.93248@ns.interchange.ca> Try octanol -help -verbose then you see that you get some "-graph related qualifiers", and you can use -goutfile2 to specify an output file. Stefanie > Hi, > > Is there a way to redirect octanol output to a filename of my > choosing? I looked through the Command line docs but couldn't > find anything. I thought there was a global option like -output > or -outfile, but I can't seem to get anything to work with > octanol. All output is named octanol.1.png (used -graph png > option). Simple enough to add a second line of code to rename the > file, but seems different than the other programs I have used so > far. > > While I am at it, I have one file with many sequences, in fasta > format. Can octanol create output for all the sequences with one > call? I can easily get around this as well, but many programs > seem to take files with many sequences, thought I would ask. > > Thanks, _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From stefanielager at fastmail.ca Tue Mar 18 01:12:05 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Tue, 18 Mar 2003 01:12:05 -0500 (EST) Subject: EMBL and Ensembl Message-ID: <3E76B8B5.00017F.99699@ns.interchange.ca> Hi, I have some problems with the EMBL format output from Ensembl. If I retrieve a LARGE piece of DNA from Ensembl in EMBL format, the SQ line gets so long so it's divided into two SQ lines, this is NOT handled correctly by EMBOSS programs! Some EMBOSS programs gives a warning about illegal characters, others just incorporates the second SQ line in the sequence. It's easy to fix the problem by manual editing, but it would be nice to know it this IS standard EMBL format or if it's Ensembl that's made a mistake? ID 1.77242832-92443803 ENSEMBL; DNA; PLN; 15200972 BP. XX ..... ..... ..... FT misc_feature 14757170..15200972 FT /note="contig 1.92000001-93000000 1..443803(1)" XX SQ Sequence 15200972 BP; 4106479 A; 3111667 C; 3123445 G; 4136833 T; 722548 SQ other; TAGAACTTGC AAATGAGAAA ACAGAGTTCT GTCAAGCTGT GTTAGTGTTT GCCCAACACA 60 _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From Jack.Leunissen at wur.nl Tue Mar 18 05:14:31 2003 From: Jack.Leunissen at wur.nl (Jack Leunissen) Date: Tue, 18 Mar 2003 11:14:31 +0100 Subject: EMBL and Ensembl References: <3E76B8B5.00017F.99699@ns.interchange.ca> Message-ID: <001201c2ed37$2b530340$6b82e089@leunissen> This is definitely NOT correct. There can be only 1 (one) SQ line per entry (see the EMBL user manual ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt). So it is Ensembl that is introducing the mistake; the EMBOSS are right in expecting only one SQ in the entry. Cheers, Jack ----- Original Message ----- From: "Stefanie Lager" To: Sent: Tuesday, March 18, 2003 7:12 AM Subject: EMBL and Ensembl > Hi, > > I have some problems with the EMBL format output from Ensembl. If I > retrieve a LARGE piece of DNA from Ensembl in EMBL format, the SQ line > gets so long so it's divided into two SQ lines, this is NOT handled > correctly by EMBOSS programs! Some EMBOSS programs gives a warning > about illegal characters, others just incorporates the second SQ line > in the sequence. It's easy to fix the problem by manual editing, but > it would be nice to know it this IS standard EMBL format or if it's > Ensembl that's made a mistake? > > ID 1.77242832-92443803 ENSEMBL; DNA; PLN; 15200972 BP. > XX > ..... > ..... > ..... > FT misc_feature 14757170..15200972 > FT /note="contig 1.92000001-93000000 1..443803(1)" > XX > SQ Sequence 15200972 BP; 4106479 A; 3111667 C; 3123445 G; 4136833 T; > 722548 > SQ other; > TAGAACTTGC AAATGAGAAA ACAGAGTTCT GTCAAGCTGT GTTAGTGTTT GCCCAACACA > 60 > > > _________________________________________________________________ > http://fastmail.ca/ - Fast Secure Web Email for Canadians From ame at esbs.u-strasbg.fr Tue Mar 18 05:52:07 2003 From: ame at esbs.u-strasbg.fr (Jean-Christophe AME) Date: Tue, 18 Mar 2003 11:52:07 +0100 Subject: problem with Apple X11beta3 and emboss Message-ID: Hi All, This morning I updated Apple X11 for MAcOSX to beta3 and now when I use an EMBOSS program does require X11 I get the following error: Error in XCreatePixmap: BadDrawable (invalid Pixmap or Window parameter). I recompiled the whole EMBOSS suite with the new AppleX11beta3 SDK but I get the same error. Can someone explain... Is it a problem with Apple X11. It used to work fine before. All the other X11 applications seem to work fine with the beta3. Thanks Jean-Christophe ________________________ Jean-Christophe Am?, PhD U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et Structurale ?cole Sup?rieure de Biotechnologie de Strasbourg P?le API Boulevard S?bastien-Brant 67400 Illkirch France tel.: 33 3 90 24 47 05 Fax.: 33 3 90 24 46 86 http://parplink.u-strasbg.fr http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1008 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20030318/6a94cdca/attachment.bin From bemis at io.iol.unh.edu Tue Mar 18 10:06:05 2003 From: bemis at io.iol.unh.edu (Matthew H. Bemis) Date: Tue, 18 Mar 2003 10:06:05 -0500 (EST) Subject: cDNA Vector trim. Message-ID: Hello, I have never used emboss before, and I would like to know if there exists a trimming program to cut a vector off some sequence samples I have, and stop trimming at my LokI site. I've compiled the full set of tools on a new Mac OSX, and I have all of them available to me. any advice would be greatly appreciated thanks, matt bemis From d.m.a.martin at dundee.ac.uk Tue Mar 18 10:26:36 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Tue, 18 Mar 2003 15:26:36 +0000 Subject: cDNA Vector trim. In-Reply-To: Message-ID: On 18/3/03 3:06 pm, "Matthew H. Bemis" wrote: > Hello, > I have never used emboss before, and I would like to know if there exists > a trimming program to cut a vector off some sequence samples I have, and > stop trimming at my LokI site. I've compiled the full set of tools on a > new Mac OSX, and I have all of them available to me. > any advice would be greatly appreciated $ wossname vector Finds programs by keywords in their one-line documentation SEARCH FOR 'VECTOR' vectorstrip Strips out DNA between a pair of vector sequences regards ..d > thanks, > matt bemis > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From alfons at elmeuportal.net Tue Mar 18 11:36:08 2003 From: alfons at elmeuportal.net (alfons at elmeuportal.net) Date: Tue, 18 Mar 2003 09:36:08 -0700 (MST) Subject: Help! Message-ID: <1224.158.109.54.199.1048005368.squirrel@www.elmeuportal.net> Hi! I would want to know if exist a program, in emboss, that make groups of genes functions in the cromosome of Drosophyla. Thanks, Alfons. From gvasudevan at medarex.com Wed Mar 19 12:39:03 2003 From: gvasudevan at medarex.com (Vasudevan, Geetha) Date: Wed, 19 Mar 2003 09:39:03 -0800 Subject: multiple seqs in fasta fmt... Message-ID: <8249C3256E593D4FB066BB9998D9F7E41CF165@ca2-fs03.ca2.2k.medarex.com> Is it possible to read multiple seqs in fasta fmt to the emboss program "pepinfo" to produce a -goutfile for hydropathy values ? thanks in advance. -geetha. From pmr at ebi.ac.uk Wed Mar 19 12:43:38 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 19 Mar 2003 17:43:38 +0000 Subject: multiple seqs in fasta fmt... References: <8249C3256E593D4FB066BB9998D9F7E41CF165@ca2-fs03.ca2.2k.medarex.com> Message-ID: <3E78AC4A.8060602@ebi.ac.uk> Vasudevan, Geetha wrote: > Is it possible to read multiple seqs in fasta fmt to the emboss program "pepinfo" > to produce a -goutfile for hydropathy values ? No ... because pepinfo creates two graphs and making that work for multiple sequence input is very tricky. This is why pepinfo only reads a single sequence (but you can put ":id" after the filename to say which FASTA file entry you want, of use dbifasta to index the file as a database) But ... it is (relatively) easy to modify pepwindow to generate hydropathy plots or data for multiple sequences. How many sequences do you have in mind? regards, Peter From Wiepert.Mathieu at mayo.edu Wed Mar 19 12:47:50 2003 From: Wiepert.Mathieu at mayo.edu (Wiepert, Mathieu) Date: Wed, 19 Mar 2003 11:47:50 -0600 Subject: multiple seqs in fasta fmt... Message-ID: <2F41CC6C9777D311ACBD009027B108EA0541C5CB@excsrv32.mayo.edu> Hi, This may be simplistic, but I had the same problem with octanol, many fasta formatted sequence in one file. so I used seqretsplit on the file, and then did this at a command line for i in *.fasta;do octanol -sequence $i -graph png ?auto -goutfile2 $i.png;done Not pretty, but it worked. -mat -----Original Message----- From: Peter Rice [mailto:pmr at ebi.ac.uk] Sent: Wednesday, March 19, 2003 11:44 AM To: Vasudevan, Geetha Cc: emboss at hgmp.mrc.ac.uk Subject: Re: multiple seqs in fasta fmt... Vasudevan, Geetha wrote: > Is it possible to read multiple seqs in fasta fmt to the emboss program "pepinfo" > to produce a -goutfile for hydropathy values ? No ... because pepinfo creates two graphs and making that work for multiple sequence input is very tricky. This is why pepinfo only reads a single sequence (but you can put ":id" after the filename to say which FASTA file entry you want, of use dbifasta to index the file as a database) But ... it is (relatively) easy to modify pepwindow to generate hydropathy plots or data for multiple sequences. How many sequences do you have in mind? regards, Peter From pmr at ebi.ac.uk Wed Mar 19 12:50:20 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 19 Mar 2003 17:50:20 +0000 Subject: multiple seqs in fasta fmt... References: <2F41CC6C9777D311ACBD009027B108EA0541C5CB@excsrv32.mayo.edu> Message-ID: <3E78ADDC.9080606@ebi.ac.uk> Wiepert, Mathieu wrote: > Hi, > > This may be simplistic, but I had the same problem with octanol, many fasta formatted sequence in one file. so I used seqretsplit on the file, and then did this at a command line > > for i in *.fasta;do octanol -sequence $i -graph png ?auto -goutfile2 $i.png;done I suspect the question is how to get all the plots into one postscript file - which means reading the full FASTA file in one run ... but this would be a good approach too. Peter From gvasudevan at medarex.com Wed Mar 19 13:16:40 2003 From: gvasudevan at medarex.com (Vasudevan, Geetha) Date: Wed, 19 Mar 2003 10:16:40 -0800 Subject: multiple seqs in fasta fmt... Message-ID: <8249C3256E593D4FB066BB9998D9F7E41CF166@ca2-fs03.ca2.2k.medarex.com> I would like to use pepinfo rather than pepwindow because, pepwindow uses Enakai.dat (Kyte-DooLittle) and I want to use Eaa_hydropathy.dat(consensus Eisenberg) used by pepinfo. pepwindow -datafile Eaa_hydropathy.dat ( raises exception-- Uncaught exception: Assertion failed, raised at ajmem.c:93) And I have 100s of seqs to calculate this. -GV -----Original Message----- From: Peter Rice [mailto:pmr at ebi.ac.uk] Sent: Wed 3/19/2003 9:43 AM To: Vasudevan, Geetha Cc: emboss at hgmp.mrc.ac.uk Subject: Re: multiple seqs in fasta fmt... Vasudevan, Geetha wrote: > Is it possible to read multiple seqs in fasta fmt to the emboss program "pepinfo" to produce a -goutfile for hydropathy values ? No ... because pepinfo creates two graphs and making that work for multiple sequence input is very tricky. This is why pepinfo only reads a single sequence (but you can put ":id" after the filename to say which FASTA file entry you want, of use dbifasta to index the file as a database) But ... it is (relatively) easy to modify pepwindow to generate hydropathy plots or data for multiple sequences. How many sequences do you have in mind? regards, Peter From gvasudevan at medarex.com Wed Mar 19 14:12:26 2003 From: gvasudevan at medarex.com (Vasudevan, Geetha) Date: Wed, 19 Mar 2003 11:12:26 -0800 Subject: index fasta DB file.. Message-ID: <8249C3256E593D4FB066BB9998D9F7E41CF168@ca2-fs03.ca2.2k.medarex.com> Is is possible to index using dbifasta, a fasta DB file whose header is like this, (>DBID 00001, species followed by description) ? And, is it possible to "retrieve" a sequence from this file, given a "DBID number"? thanks for all your suggestions. -Geetha. From kellert at ohsu.edu Wed Mar 19 18:12:45 2003 From: kellert at ohsu.edu (Thomas Keller) Date: Wed, 19 Mar 2003 15:12:45 -0800 Subject: microarray primer design Message-ID: <4B68B919-5A60-11D7-8736-0003930405E2@ohsu.edu> I've always designed primers one at a time. Usually with the very excellent program Oligo (W. Rychlik). I've got eprimer3/primer3 working but I'm not sure how to use it to find hybridization oligos for use with microarrays. I'd be grateful for suggestions, since I've got about 1,300 oligos to design. Thanks, Tom K. From grimplet at ensam.inra.fr Thu Mar 20 03:10:56 2003 From: grimplet at ensam.inra.fr (=?iso-8859-1?q?j=E9r=F4me=20Grimplet?=) Date: Thu, 20 Mar 2003 09:10:56 +0100 Subject: microarray primer design In-Reply-To: <4B68B919-5A60-11D7-8736-0003930405E2@ohsu.edu> References: <4B68B919-5A60-11D7-8736-0003930405E2@ohsu.edu> Message-ID: <200303200910.56160.grimplet@ensam.inra.fr> Le Jeudi 20 Mars 2003 00:12, Thomas Keller a ?crit : > I've always designed primers one at a time. Usually with the very > excellent program Oligo (W. Rychlik). > I've got eprimer3/primer3 working but I'm not sure how to use it to > find hybridization oligos for use with microarrays. > I'd be grateful for suggestions, since I've got about 1,300 oligos to > design. > Thanks, > Tom K. Hi, Try OligoArray...... http://berry.engin.umich.edu/oligoarray/ -- J?r?me Grimplet Laboratoire de Biochimie M?tabolique et Technologie UMR Sciences Pour l'Oenologie 2, Place Viala 34060 Montpellier Cedex 01 Tel: 33(0)4.99.61.27.56 Fax: 33(0)4.99.61.28.57 grimplet at ensam.inra.fr From gwilliam at hgmp.mrc.ac.uk Thu Mar 20 04:28:20 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 20 Mar 2003 09:28:20 +0000 Subject: microarray primer design References: <4B68B919-5A60-11D7-8736-0003930405E2@ohsu.edu> Message-ID: <3E7989B4.EA92BA49@hgmp.mrc.ac.uk> Microarrays typically use oligos of about 50 to 60 bp in length. The maximum length of an oligo that can be found by the primer3 program is 35. This limit is governed by the maximum oligo size for which primer3's melting-temperature is valid. Gary Thomas Keller wrote: > > I've always designed primers one at a time. Usually with the very > excellent program Oligo (W. Rychlik). > I've got eprimer3/primer3 working but I'm not sure how to use it to > find hybridization oligos for use with microarrays. > I'd be grateful for suggestions, since I've got about 1,300 oligos to > design. > Thanks, > Tom K. -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From pmr at ebi.ac.uk Thu Mar 20 06:44:43 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Mar 2003 11:44:43 +0000 Subject: multiple seqs in fasta fmt... References: <8249C3256E593D4FB066BB9998D9F7E41CF166@ca2-fs03.ca2.2k.medarex.com> Message-ID: <3E79A9AB.8080408@ebi.ac.uk> Vasudevan, Geetha wrote: > I would like to use pepinfo rather than pepwindow because, > pepwindow uses Enakai.dat (Kyte-DooLittle) and I want to use > Eaa_hydropathy.dat(consensus Eisenberg) used by pepinfo. > pepwindow -datafile Eaa_hydropathy.dat ( raises exception-- > Uncaught exception: Assertion failed, raised at ajmem.c:93) > > And I have 100s of seqs to calculate this. Ah ... but pepwindow can use any of the "Nakai et al." database of amino acid parameters - these used to be in a database called "NAKAI" but are now in one called "AAINDEX". EMBOSS has a program "aaindexextract" that takes data from this database and makes it available for pepwindow. It appears this enhancement did not make it into the pepwindow documentation... it will do today!!! 1. FTP the AAINDEX database from Japan: ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1 2. Run aaindexextract with the aaindex1 file as input (or ask whoever installs EMBOSS to run it) 3. Run pepwindow with -datafile swer830101 and (to match pepinfo) -hwindow 9 (or whatever value you use for -length in pepinfo) This is the middle plot pepinfo produces. ... and of course we should look into why pepinfo and pepwindow use different window lengths, and different option names. Hope this helps. Peter Rice From bemis at io.iol.unh.edu Thu Mar 20 09:47:51 2003 From: bemis at io.iol.unh.edu (Matthew H. Bemis) Date: Thu, 20 Mar 2003 09:47:51 -0500 (EST) Subject: cDNA Vector trim. In-Reply-To: References: Message-ID: Hi, Thanks for the advice! The programs work great. Now I have all this data and I have phred( phd.1 ) files that I'd like to align and look for mismatches( high score mismatches ). Is there software for this? I have four file types to work with here: .seq fasta phd.1 scf if there software out there for looking for high quality mutations? writing software is not out of the question for me either. I am a cs graduate student, but I'd rather not re-invent the wheel. thanks in advance! Matt Bemis On Tue, 18 Mar 2003, David Martin wrote: > On 18/3/03 3:06 pm, "Matthew H. Bemis" wrote: > > > Hello, > > I have never used emboss before, and I would like to know if there exists > > a trimming program to cut a vector off some sequence samples I have, and > > stop trimming at my LokI site. I've compiled the full set of tools on a > > new Mac OSX, and I have all of them available to me. > > any advice would be greatly appreciated > > $ wossname vector > Finds programs by keywords in their one-line documentation > SEARCH FOR 'VECTOR' > vectorstrip Strips out DNA between a pair of vector sequences > > > regards > > ..d > > > thanks, > > matt bemis > > > > -- > David Martin PhD > Bioinformatics Scientific Officer > Post-Genomics and Molecular Interactions Centre > University of Dundee > From mad at biol.unlp.edu.ar Thu Mar 20 10:06:11 2003 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Thu, 20 Mar 2003 12:06:11 -0300 Subject: =?ISO-8859-1?Q?=BFEMBOSS_first_release=3F?= Message-ID: <3E79D8E3.4090107@biol.unlp.edu.ar> Hi, I'm preparing a presentation on EMBOSS and I would like to know when was the first release of it. In http://www.emboss.org in the "History" page isn't mentioned, only that it evolved from EGCG. Thanks. Regards, martin -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From lmullan at hgmp.mrc.ac.uk Thu Mar 20 10:05:04 2003 From: lmullan at hgmp.mrc.ac.uk (Lisa Mullan) Date: Thu, 20 Mar 2003 15:05:04 +0000 (GMT) Subject: =?ISO-8859-1?Q?=BFEMBOSS_first_release=3F?= In-Reply-To: <3E79D8E3.4090107@biol.unlp.edu.ar> Message-ID: As far as I know it was St. Swithans Day (15th July) 2000 - that's what I tell people on the courses, so unless Alan was drunk when he told me................!! Lisa PS: If you need any material, let me know. Lisa Mullan HGMP Resource Centre Hinxton, Cambridge, CB10 1SB Tel: 01223 494526 Email: lmullan at hgmp.mrc.ac.uk On Thu, 20 Mar 2003, [ISO-8859-1] Mart?n Sarachu wrote: > Hi, > > I'm preparing a presentation on EMBOSS and I would like to know when was > the first release of it. In http://www.emboss.org in the "History" page > isn't mentioned, only that it evolved from EGCG. > > Thanks. > > > Regards, > > martin > > -- > Mart?n Sarachu > mad at biol.unlp.edu.ar > EMBNet Argentina > http://www.ar.embnet.org > From pmr at ebi.ac.uk Thu Mar 20 10:06:03 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Mar 2003 15:06:03 +0000 Subject: =?ISO-8859-1?Q?=BFEMBOSS_first_release=3F?= References: <3E79D8E3.4090107@biol.unlp.edu.ar> Message-ID: <3E79D8DB.7010504@ebi.ac.uk> Mart?n Sarachu wrote: > I'm preparing a presentation on EMBOSS and I would like to know when was > the first release of it. In http://www.emboss.org in the "History" page > isn't mentioned, only that it evolved from EGCG. I remember it well. EMBOSS 1.0.0 was July 15th 2000. Saint Swithin's Day ... and the day I handed over the project to Alan when I left the Sanger Centre. Of course, the beta versions were around for a couple of years before that. I demonstrated 0.0.c (if memory serves) in August 1998. Alan ... do you have a copy of the announcement? Maybe it could go on the website :-) regards, Peter From d.m.a.martin at dundee.ac.uk Thu Mar 20 10:10:48 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 20 Mar 2003 15:10:48 +0000 Subject: cDNA Vector trim. In-Reply-To: Message-ID: On 20/3/03 2:47 pm, "Matthew H. Bemis" wrote: > Hi, > Thanks for the advice! The programs work great. Now I have all this data > and I have phred( phd.1 ) files that I'd like to align and look for > mismatches( high score mismatches ). Is there software for this? > I have four file types to work with here: > .seq > fasta > phd.1 > scf > if there software out there for looking for high quality mutations? > writing software is not out of the question for me either. I am a cs > graduate student, but I'd rather not re-invent the wheel. > thanks in advance! Checkout the staden package which does all sorts of things you would find useful, in particular pregap4 and gap4. ..d > Matt Bemis > > On Tue, 18 Mar 2003, David Martin wrote: > >> On 18/3/03 3:06 pm, "Matthew H. Bemis" wrote: >> >>> Hello, >>> I have never used emboss before, and I would like to know if there exists >>> a trimming program to cut a vector off some sequence samples I have, and >>> stop trimming at my LokI site. I've compiled the full set of tools on a >>> new Mac OSX, and I have all of them available to me. >>> any advice would be greatly appreciated >> >> $ wossname vector >> Finds programs by keywords in their one-line documentation >> SEARCH FOR 'VECTOR' >> vectorstrip Strips out DNA between a pair of vector sequences >> >> >> regards >> >> ..d >> >>> thanks, >>> matt bemis >>> >> >> -- >> David Martin PhD >> Bioinformatics Scientific Officer >> Post-Genomics and Molecular Interactions Centre >> University of Dundee >> > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From d.m.a.martin at dundee.ac.uk Thu Mar 20 10:14:40 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 20 Mar 2003 15:14:40 +0000 Subject: =?ISO-8859-1?B?vw==?=EMBOSS first release? In-Reply-To: Message-ID: On 20/3/03 3:05 pm, "Lisa Mullan" wrote: > As far as I know it was St. Swithans Day (15th July) 2000 - that's what I > tell people on the courses, so unless Alan was drunk when he told > me................!! > Well I would have been as that was my birthday.. That was release 1.0.0 AFAIR. 0.0.4 was floating around for at least a year before that (and earlier incarnations before that). The first useable production release is a more subjective question.. probably about christmas 1999. The changes were flying thick and fast back then.. 2 or three updates a week. ..d > Lisa > > > PS: If you need any material, let me know. > > Lisa Mullan > HGMP Resource Centre > Hinxton, > Cambridge, CB10 1SB > Tel: 01223 494526 > Email: lmullan at hgmp.mrc.ac.uk > > On Thu, 20 Mar 2003, [ISO-8859-1] Mart?n Sarachu wrote: > >> Hi, >> >> I'm preparing a presentation on EMBOSS and I would like to know when was >> the first release of it. In http://www.emboss.org in the "History" page >> isn't mentioned, only that it evolved from EGCG. >> >> Thanks. >> >> >> Regards, >> >> martin >> >> -- >> Mart?n Sarachu >> mad at biol.unlp.edu.ar >> EMBNet Argentina >> http://www.ar.embnet.org >> > > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From ableasby at hgmp.mrc.ac.uk Thu Mar 20 10:15:55 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 20 Mar 2003 15:15:55 GMT Subject: =?ISO-8859-1?Q?=BFEMBOSS_first_release=3F?= Message-ID: <200303201515.h2KFFtF21824@bromine.hgmp.mrc.ac.uk> I'll see if I can find an announcement but I'm not hopeful. As for being drunk, Lisa knows perfectly well that I don't drink alcohol (others may not). Cheers Alan From gwilliam at hgmp.mrc.ac.uk Thu Mar 20 10:19:16 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 20 Mar 2003 15:19:16 +0000 Subject: =?iso-8859-1?Q?=BFEMBOSS?= first release? References: <200303201515.h2KFFtF21824@bromine.hgmp.mrc.ac.uk> Message-ID: <3E79DBF4.204850BC@hgmp.mrc.ac.uk> Announcement attached. Gary ableasby at hgmp.mrc.ac.uk wrote: > > I'll see if I can find an announcement but I'm not hopeful. > > As for being drunk, Lisa knows perfectly well that I don't > drink alcohol (others may not). > > Cheers > Alan -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK -------------- next part -------------- From pmiguel at purdue.edu Thu Mar 20 10:16:47 2003 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Thu, 20 Mar 2003 10:16:47 -0500 Subject: cDNA Vector trim. References: Message-ID: <3E79DB5F.3090400@purdue.edu> David Martin wrote: >On 20/3/03 2:47 pm, "Matthew H. Bemis" wrote: > > > >>Hi, >>Thanks for the advice! The programs work great. Now I have all this data >>and I have phred( phd.1 ) files that I'd like to align and look for >>mismatches( high score mismatches ). Is there software for this? >>I have four file types to work with here: >>.seq >>fasta >>phd.1 >>scf >>if there software out there for looking for high quality mutations? >>writing software is not out of the question for me either. I am a cs >>graduate student, but I'd rather not re-invent the wheel. >>thanks in advance! >> >> > >Checkout the staden package which does all sorts of things you would find >useful, in particular pregap4 and gap4. > >..d > [...] If you have the phredPhrap package already, you might find cross_match sufficient. Convert your phd files to a fasta and qual files using phd2fasta. When you do the comparsion with cross_match, a large table of the quality values of the mis-matches is generated. Not sure if it is what you are looking for. I generally am looking for ways to filter out this output. Help is at www.phrap.org. Phillip SanMiguel Purdue Genomics Core From d.m.a.martin at dundee.ac.uk Thu Mar 20 10:22:28 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 20 Mar 2003 15:22:28 +0000 Subject: FW: EMBOSS has moved to HGMP In-Reply-To: <200007152229.XAA19252@bromine.hgmp.mrc.ac.uk> Message-ID: Here is the move from Sanger to HGMP and a hint of a 1.0 release -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee ------ Forwarded Message From: Date: Sat, 15 Jul 2000 23:29:33 +0100 (BST) To: emboss at hgmp.mrc.ac.uk Subject: EMBOSS has moved to HGMP Dear EMBOSS folk, Yes, EMBOSS has indeed moved. Please note the new address for the web pages. It is: http://www.uk.embnet.org/Software/EMBOSS or if you prefer http://www.hgmp.mrc.ac.uk/Software/EMBOSS they are the same address. Similarly the ftp server becomes: ftp://ftp.uk.embnet.org/pub/EMBOSS or ftp://ftp.hgmp.mrc.ac.uk/pub/EMBOSS Why the move? It is because Peter Rice and Ian Longden have both just gone into the commercial sector. Peter has gone to Lion and Ian to Informatica. This left noone at Sanger with the experience to maintain EMBOSS therefore it finds a welcome home with the HGMP developers. I surely speak for all of us when I thank Peter and Ian for their work... although Peter will still be active with EMBOSS from the Lion point of view so this is neither an obituary or E.J. Thribb poem. Both still have their Sanger usernames intact for now. And so on to the changes. You will notice a different look and feel to the web pages. This is in preparation for the imminent announcement of Release 1.0.0. You will see this reflected in the filename of EMBOSS on the ftp server. It is EMBOSS-1.0.0.tar.gz N.B: As of this distribution there is an extra 'emboss' directory level at the top. This is to allow the --prefix configuration option to (optionally) install directories there. The instructions for use of the CVS server have also changed. Please read the new instructions on the web pages if you use this method. This server also has the extra directory mentioned above. Also note that there is no alias for cvs.hgmp.mrc.ac.uk at the moment i.e. cvs.uk.embnet.org will not work but the former will. The mail list addresses have changed accordingly. They are: emboss at uk.embnet.org emboss-dev at uk.embnet.org or emboss at hgmp.mrc.ac.uk emboss-dev at hgmp.mrc.ac.uk All the subscription addresses have been moved over. The majordomo server at our site works in the same way as on the Sanger site. N.B.: Until the Sanger site change their links to redirect to HGMP their site is still active. It is not being updated though. To get the latest updates you must use the new addresses. I am bound to have forgotten something as we've all had to work like demons to move things over and get to a stage where we can advertise release 1.0.0. I will post if anything important springs to mind. Finally, it is St Swithins Day so, if the new service works today it will probably work for the next 40. If not you can always email: emboss-bug at uk.embnet.org or emboss-bug at hgmp.mrc.ac.uk Cheers Alan HGMP ------ End of Forwarded Message From lmullan at hgmp.mrc.ac.uk Thu Mar 20 10:24:48 2003 From: lmullan at hgmp.mrc.ac.uk (Lisa Mullan) Date: Thu, 20 Mar 2003 15:24:48 +0000 (GMT) Subject: =?ISO-8859-1?Q?=BFEMBOSS_first_release=3F?= In-Reply-To: <200303201515.h2KFFtF21824@bromine.hgmp.mrc.ac.uk> Message-ID: Exactly - so everyone knows that what you told me must be true!!! Lisa Lisa Mullan HGMP Resource Centre Hinxton, Cambridge, CB10 1SB Tel: 01223 494526 Email: lmullan at hgmp.mrc.ac.uk On Thu, 20 Mar 2003 ableasby at hgmp.mrc.ac.uk wrote: > I'll see if I can find an announcement but I'm not hopeful. > > As for being drunk, Lisa knows perfectly well that I don't > drink alcohol (others may not). > > Cheers > Alan > From pmr at ebi.ac.uk Thu Mar 20 11:15:04 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Mar 2003 16:15:04 +0000 Subject: index fasta DB file.. References: <8249C3256E593D4FB066BB9998D9F7E41CF168@ca2-fs03.ca2.2k.medarex.com> Message-ID: <3E79E908.4080305@ebi.ac.uk> Vasudevan, Geetha wrote: > Is is possible to index using dbifasta, a fasta DB file whose header is like this, > > (>DBID 00001, species followed by description) ? > > And, is it possible to "retrieve" a sequence from this file, given a "DBID number"? The syntax must match something dbifasta understands. See the dbifasta documentation for more information. DBID should be some 'standard' fasta identifier. EMBOSS is happy with anything in test/data/testids.fasta or test/data/testids.ncbi For example: >dbname:id or >id In both cases, filename:id will extract that ID You can also read the accession number, if it appears as the next text on the line: >DBID A00001 species followed by description then you can use filename:a00001 ... but this only works if (a) the accession number is a valid EMBL/SwissProt accession number and (b) it has white space either side. This format of fasta file is (or was) used by ACEDB at the Sanger Centre. Hope this helps, Peter Rice From gwilliam at hgmp.mrc.ac.uk Thu Mar 20 11:50:48 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 20 Mar 2003 16:50:48 +0000 Subject: =?iso-8859-1?Q?=BFEMBOSS?= first release? References: <3E79D8E3.4090107@biol.unlp.edu.ar> Message-ID: <3E79F168.8F10DAD8@hgmp.mrc.ac.uk> Some of the early milestones for EMBOSS are now documented briefly in: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/history.html Gary Mart?n Sarachu wrote: > > Hi, > > I'm preparing a presentation on EMBOSS and I would like to know when was > the first release of it. In http://www.emboss.org in the "History" page > isn't mentioned, only that it evolved from EGCG. > > Thanks. > > Regards, > > martin > > -- > Mart?n Sarachu > mad at biol.unlp.edu.ar > EMBNet Argentina > http://www.ar.embnet.org -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From aengus.stewart at cancer.org.uk Thu Mar 20 12:27:31 2003 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Thu, 20 Mar 2003 17:27:31 +0000 Subject: DataLib management Message-ID: <3E79FA03.F529F703@cancer.org.uk> Hi, Sorry in advance folks, but I am making a concerted effort to set up the datalibs for access by EMBOSS and as a result it has prompted a few questions. First of all a comment - I have had a look at the documentation for both dbiflat and dbigcg, and neither makes any note of the fact that both ACNUM and ID fields are indexed by default. In fact ID is not really mentioned at all so when you look at the documentation for the '-fields' flag it appears that there are only 5 possible fields to index. A small point, there is an inconsistency between the allowed values for -fields and the values for the fields: tag in emboss.default -fields flag can use any of - acnum,seqvn,des,keyword,taxon fields: tag can use any of - acc id sv des org key I know they dont have to be the same, it just seemed odd. showdb -fields returns Died: unknown qualifier -fields Also dbigcg/dbiflat asks for the release number and date. I would like showdb to pick this information up but the only way I can see of doing this is a search/replace on 'release:X.Y' in emboss.default What does dbigcg/dbiflat do with the release/date info? Sorry again for all the queries. Aengus -- -------------------------------------------------------------------------- Aengus Stewart aengus.stewart at DELcancerETE.org.uk Computational Genome Analysis Laboratory Tel: +44 (0)20 7269 3679 Cancer Research UK Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK -------------------------------------------------------------------------- From pmr at ebi.ac.uk Thu Mar 20 12:35:03 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Mar 2003 17:35:03 +0000 Subject: DataLib management References: <3E79FA03.F529F703@cancer.org.uk> Message-ID: <3E79FBC7.7050508@ebi.ac.uk> Aengus Stewart wrote: > First of all a comment - I have had a look at the documentation for both > dbiflat and dbigcg, and neither makes any note of the fact that both > ACNUM and ID fields are indexed by default. Will be fixed. Thanks. > A small point, there is an inconsistency between the allowed values for > -fields and the values for the fields: tag in emboss.default > > I know they dont have to be the same, it just seemed odd. Should be consistent. One is the names for the query syntax (same as in SRS) the other is the name used in the EMBLCD format index files. I would prefer to use the query language names (id acc sv des org key) which means just changing the prompts for dbiflat and friends. Any other votes? > showdb -fields > returns > Died: unknown qualifier -fields This works in the current developers release, which is what the EMBOSS web pages always refer to. > What does dbigcg/dbiflat do with the release/date info? It is part of the EMBLCD (and Staden) index file header. EMBOSS does not use it at present - but I would like to start making use of it. It is not yet clear whether there should be a release number in the DBNAME definition in emboss.defaults - it is convenient to save asking the EMBLCD index (or SRS or whatever) but would need to be maintained. Let's just say "I'm working on a solution" :-) Hope this helps, Peter From aengus.stewart at cancer.org.uk Fri Mar 21 09:39:55 2003 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Fri, 21 Mar 2003 14:39:55 +0000 Subject: Non-sequence DataLibs References: <3E79FA03.F529F703@cancer.org.uk> Message-ID: <3E7B243B.9A97188A@cancer.org.uk> Hi, I was wondering whether EMBOSS has plans to handle biological structured record data like GO, UNIGENE etc. I was playing around with setting up DBs with methodquery:srswww format: text url:"http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz" but of course retrieving things with seqret doesnt work and entret just produces an empty file. Regards Aengus From ableasby at hgmp.mrc.ac.uk Fri Mar 21 09:50:48 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 21 Mar 2003 14:50:48 GMT Subject: Non-sequence DataLibs Message-ID: <200303211450.h2LEomw28312@bromine.hgmp.mrc.ac.uk> New fields have recently been added to the emboss.defaults definitions as a preliminary step towards handling non-sequence datalibs. So, the answer is that the intention is there but its in the very early stages of development. Alan From aengus.stewart at cancer.org.uk Fri Mar 21 12:51:35 2003 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Fri, 21 Mar 2003 17:51:35 +0000 Subject: Problem with EMBOSS_ROOT References: <200303211450.h2LEomw28312@bromine.hgmp.mrc.ac.uk> Message-ID: <3E7B5127.DA2F05F8@cancer.org.uk> I know its Friday and its well past 5 O'clock but....... I have instances of EMBOSS on 2 machines with the same OS/setup so I just copied the bin/lib/share and then attempted export EMBOSS_ROOT=/path/to/dir/containing/emboss.default on the non-compilation machine unfortunately showdb wasnt too happy. I did separate compilations to sort it but I thought I should mention the EMBOSS_ROOT problem. Aengus -- -------------------------------------------------------------------------- Aengus Stewart aengus.stewart at DELcancerETE.org.uk Computational Genome Analysis Laboratory Tel: +44 (0)20 7269 3679 Cancer Research UK Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK -------------------------------------------------------------------------- From bemis at io.iol.unh.edu Sat Mar 22 12:25:09 2003 From: bemis at io.iol.unh.edu (Matthew H. Bemis) Date: Sat, 22 Mar 2003 12:25:09 -0500 (EST) Subject: cDNA Vector trim. In-Reply-To: References: Message-ID: David, thanks for the info. I've read up on gap4, and it does look like I'll be using this, but I am encountering XFree86 issues on our macosx server. I am an avid X user, but on linux. Using bash I export the display to the correct name, and i try to add the local host to xauth...well I really have been trying to just xhost + the world. The program gap4 will not start. any ideas?? On Thu, 20 Mar 2003, David Martin wrote: > On 20/3/03 2:47 pm, "Matthew H. Bemis" wrote: > > > Hi, > > Thanks for the advice! The programs work great. Now I have all this data > > and I have phred( phd.1 ) files that I'd like to align and look for > > mismatches( high score mismatches ). Is there software for this? > > I have four file types to work with here: > > .seq > > fasta > > phd.1 > > scf > > if there software out there for looking for high quality mutations? > > writing software is not out of the question for me either. I am a cs > > graduate student, but I'd rather not re-invent the wheel. > > thanks in advance! > > Checkout the staden package which does all sorts of things you would find > useful, in particular pregap4 and gap4. > > ..d > > > Matt Bemis > > > > On Tue, 18 Mar 2003, David Martin wrote: > > > >> On 18/3/03 3:06 pm, "Matthew H. Bemis" wrote: > >> > >>> Hello, > >>> I have never used emboss before, and I would like to know if there exists > >>> a trimming program to cut a vector off some sequence samples I have, and > >>> stop trimming at my LokI site. I've compiled the full set of tools on a > >>> new Mac OSX, and I have all of them available to me. > >>> any advice would be greatly appreciated > >> > >> $ wossname vector > >> Finds programs by keywords in their one-line documentation > >> SEARCH FOR 'VECTOR' > >> vectorstrip Strips out DNA between a pair of vector sequences > >> > >> > >> regards > >> > >> ..d > >> > >>> thanks, > >>> matt bemis > >>> > >> > >> -- > >> David Martin PhD > >> Bioinformatics Scientific Officer > >> Post-Genomics and Molecular Interactions Centre > >> University of Dundee > >> > > > > -- > David Martin PhD > Bioinformatics Scientific Officer > Post-Genomics and Molecular Interactions Centre > University of Dundee > From pmr at ebi.ac.uk Mon Mar 24 05:01:45 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 24 Mar 2003 10:01:45 +0000 Subject: Non-sequence DataLibs References: <3E79FA03.F529F703@cancer.org.uk> <3E7B243B.9A97188A@cancer.org.uk> Message-ID: <3E7ED789.9050704@ebi.ac.uk> Aengus Stewart wrote: > I was wondering whether EMBOSS has plans to handle biological structured > record data like GO, UNIGENE etc. > > I was playing around with setting up DBs with > > methodquery:srswww > format: text > url:"http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz" > > but of course retrieving things with seqret doesnt work and entret just > produces an empty file. Yes!!! As Alan said, there are already placeholders for this stuff. I am working on the internals now. Still have to think up an equivalent name to "entret" (which reads sequences as its input type and returns whole entries). "entire" perhaps?) Also need to give a little thought to how to index such databases - aside from using a remote web server (like your example) or local SRS. Hope this helps, Peter From Wiepert.Mathieu at mayo.edu Tue Mar 25 11:05:35 2003 From: Wiepert.Mathieu at mayo.edu (Wiepert, Mathieu) Date: Tue, 25 Mar 2003 10:05:35 -0600 Subject: dbiflat dies...can I restart where it left off? Message-ID: <2F41CC6C9777D311ACBD009027B108EA0541C609@excsrv32.mayo.edu> Hi, I am trying to index a large set of est genbank files with dbiflat. After a few hours of processing, I got Index a flat file database EMBL : EMBL SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew GB : Genbank, DDBJ REFSEQ : Refseq Entry format [SWISS]: genbank Database directory [.]: Wildcard database filename [*.dat]: *.genbank Database name: test Release number [0.0]: .1 Index date [00/00/00]: 03/25/03 Warning: Duplicate ID skipped: 'BF291273' All hits will point to first ID found EMBOSS An error in embdbi.c at line 1074: Error in embDbiSortWriteFields, expected entry BU664328 not found Is there a way to restart this? I didn't use any of the -warning -error -fatal -die -debug options, maybe I should have, so I could see a log. I thought this might be one way to index genbank itself? I have tried bioperl for this, but it takes MUCH longer (as I might have suspected anyway). Haven't tried anything from the ncbi toolkit. -Mat From hkawai at venus.dti.ne.jp Wed Mar 26 08:31:26 2003 From: hkawai at venus.dti.ne.jp (Hironori Kawai) Date: Wed, 26 Mar 2003 22:31:26 +0900 Subject: Retrieiving DB with a list file Message-ID: <200303261330.h2QDU4ME001133@smtp4.dti.ne.jp> Hello When I retrieve some entries from databases using a list file (e.g. seqret @listfile) which consists of both retrievable USAs and irretrievable ones, I meet a kind of problem. If the top-line is a retrievable USA, I can get all retrievable entries, skipping non-retrievable ones. In contrast, if the top-line is irretrievable, programs stop immediately without retrieving any entries inspite of the existence of retrievable USAs on the following lines. I want to make the programs not to terminate even if the top-line is irretrievable. Thanks Hironori Kawai From janef_23 at hotmail.com Wed Mar 26 10:21:26 2003 From: janef_23 at hotmail.com (Jane Fowler) Date: Wed, 26 Mar 2003 15:21:26 +0000 Subject: question about prophecy and profit Message-ID: An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030326/d2e005b4/attachment.html From pmr at ebi.ac.uk Wed Mar 26 10:23:06 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 26 Mar 2003 15:23:06 +0000 Subject: Retrieiving DB with a list file References: <200303261330.h2QDU4ME001133@smtp4.dti.ne.jp> Message-ID: <3E81C5DA.3000609@ebi.ac.uk> Hironori Kawai wrote: > Hello > > When I retrieve some entries from databases using a list file > (e.g. seqret @listfile) which consists of both retrievable USAs and > irretrievable ones, I meet a kind of problem. > > I want to make the programs not to terminate even if > the top-line is irretrievable. I noticed this one a few days ago. Already fixed in the CVS developers version, and included in the set of QA tests. So "fixed in the next release". Peter From mad at biol.unlp.edu.ar Wed Mar 26 11:43:45 2003 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Wed, 26 Mar 2003 13:43:45 -0300 Subject: OT: where to download transfac database? Message-ID: <3E81D8C1.8000409@biol.unlp.edu.ar> Hi, anyone knows where to download TRANSFAC version 6 public? In the EBI mirror the latest version is TRANSFAC 3.2 Regards, martin -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From luojc at plum.lsc.pku.edu.cn Wed Mar 26 17:55:08 2003 From: luojc at plum.lsc.pku.edu.cn (Jingchu Luo) Date: Thu, 27 Mar 2003 06:55:08 +0800 (CST) Subject: OT: where to download transfac database? In-Reply-To: <3E81D8C1.8000409@biol.unlp.edu.ar> Message-ID: On Wed, 26 Mar 2003, Mart?n Sarachu wrote: > Hi, > > anyone knows where to download TRANSFAC version 6 public? > In the EBI mirror the latest version is TRANSFAC 3.2 It is run by a company BioBase and you should pay 500 euro for ver 6.0 as an academic user. Pls see details at: http://www.biobase.de/pages/products/databases.html Jingchu Luo > Regards, > > martin > > From edgar_wingender at yahoo.de Thu Mar 27 03:08:00 2003 From: edgar_wingender at yahoo.de (=?iso-8859-1?q?Edgar=20Wingender?=) Date: Thu, 27 Mar 2003 09:08:00 +0100 (CET) Subject: OT: where to download transfac database? In-Reply-To: Message-ID: <20030327080800.43028.qmail@web12201.mail.yahoo.com> Dear Dr. Sarachu, TRANSFAC 6.0 Public is available online only at http://www.gene-regulation.de For downlaoding and local (internal) installation, only the Professional version is available. The yearly license fee for this version (including 4 updates per year) is 500$ or 500 Euro for academic users. Licensing is done through BIOBASE, the address being given by Jingchu Luo is correct. Best regards, Edgar Wingender. > > On Wed, 26 Mar 2003, Mart?n Sarachu wrote: > > > Hi, > > > > anyone knows where to download TRANSFAC version 6 > public? > > In the EBI mirror the latest version is TRANSFAC > 3.2 > > It is run by a company BioBase and you should pay > 500 euro for ver 6.0 > as an academic user. Pls see details at: > > http://www.biobase.de/pages/products/databases.html > > Jingchu Luo > > > Regards, > > > > martin > > > > > > > ===== Prof. Dr. Edgar Wingender Department of Bioinformatics UKG, University of Goettingen Goldschmidtstr. 1, D-37077 Goettingen phone +49(0)-551-39-14911; fax +49(0)-551-39-14914 email e.wingender at med.uni-goettingen.de __________________________________________________________________ Gesendet von Yahoo! Mail - http://mail.yahoo.de Bis zu 100 MB Speicher bei http://premiummail.yahoo.de From d.m.a.martin at dundee.ac.uk Thu Mar 27 06:31:31 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 27 Mar 2003 11:31:31 +0000 Subject: Equivalent to diverge Message-ID: Is there an EMBOSS equivalent to the GCG diverge program? ..d -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From kim at inb.uni-luebeck.de Thu Mar 27 06:59:37 2003 From: kim at inb.uni-luebeck.de (Jan T. Kim) Date: Thu, 27 Mar 2003 12:59:37 +0100 Subject: question about prophecy and profit In-Reply-To: ; from janef_23@hotmail.com on Wed, Mar 26, 2003 at 03:21:26PM +0000 References: Message-ID: <20030327125937.B6130@pc10.inb.mu-luebeck.de> On Wed, Mar 26, 2003 at 03:21:26PM +0000, Jane Fowler wrote: > I am trying to use the prophecy and profit programs to locate a > consensus sequence in a genome. I am wondering if it is possible to > use a DNA sequence or if it must be a protein sequence to create a > frequency matrix. It would be great if someone could reply. [Note: The message was in HTML only, I had to manually cut & paste it into my email editor in order to quote it. Please send plain text messages to mailing lists.] I've run into the same question some time ago and found out that, prophecy and profit do not care at all what type of sequence (amino acid or nucleotide) is processed. In fact, these programs seem to operate generically on sequences of the letters a-z, in the source, I found no indication that the programs make any specific assumptions on what these letters denote biologically. The matrices produced by prophecy have 26 columns, not 20 for the amino acids (as I originally thought before I tried counting instead of thinking... ;-) ) The bottom line is: You can use prophecy and profit on any type of sequence, but note that you'll get nonsense if your sequences contain ambiguity codes (such as R for purine, Y for pyrimidine etc.). Greetinx, Jan -- +- Jan T. Kim -------------------------------------------------------+ | *NEW* email: kim at inb.uni-luebeck.de | | *NEW* WWW: http://www.inb.uni-luebeck.de/staff/kim.html | *-----=< hierarchical systems are for files, not for humans >=-----* From gwilliam at hgmp.mrc.ac.uk Thu Mar 27 08:53:36 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 27 Mar 2003 13:53:36 +0000 Subject: Equivalent to diverge References: Message-ID: <3E830260.C690C817@hgmp.mrc.ac.uk> No. David Martin wrote: > > Is there an EMBOSS equivalent to the GCG diverge program? -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From squiresb at macrogenics.com Thu Mar 27 19:06:24 2003 From: squiresb at macrogenics.com (Burke Squires) Date: Thu, 27 Mar 2003 18:06:24 -0600 Subject: FW: Lib error? In-Reply-To: Message-ID: Hello, I will be using EMBOSS through the REALbasic programming environment. In an effort to see if a bioteam.net package installation would behave better with the synchronous shell mode I installed EMBOSS in addition to my 2.6.0 compiled version. Now something is not connecting...anybody have any ideas: dyld: eprimer3 can't open library: /usr/local/lib/libgd.2.dylib (No such file or directory, errno = 2) Trace/BPT trap I tried changing my .cshrc files back but now go? Thanks! Burke -- Burke Squires Bioinformatics MacroGenics, Inc. 2600 Stemmons Freeway, Suite 210 Dallas, TX 75235 USA Work: 214-634-3000 X224 Fax: 214-634-3002 ---------------------------------------------------------------------------- This e-mail and any attachments may be confidential or legally privileged. If you received this message in error or are not the intended recipient, you should destroy the e-mail message and any attachments or copies, and you are prohibited from retaining, distributing, disclosing or using any information contained herein. Please inform us of the erroneous delivery by return e-mail. Thank you for your cooperation. ------ End of Forwarded Message From jrvalverde at cnb.uam.es Tue Mar 4 13:36:05 2003 From: jrvalverde at cnb.uam.es (José R. Valverde) Date: Tue, 4 Mar 2003 14:36:05 +0100 Subject: Jemboss app listing Message-ID: <20030304143605.3d72f6d6.jrvalverde@cnb.uam.es> Hi, I'm having trouble with Jemboss concerning the hierarchihcal listing of application menus in the top left side. This has been consistent for quite some time, and the problem is that the listing changes each time I start Jemboss. It seems like the Java application is getting an incomplete listing of applications, truncating the list at varying points each time Jemboss is started and offering an incomplete listing. It looks like a problem due to a short timeout waiting for the listing of applications.. Anyone knows if there is a fix for this? j From tcarver at hgmp.mrc.ac.uk Tue Mar 4 14:00:27 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Tue, 4 Mar 2003 14:00:27 +0000 (GMT) Subject: Jemboss app listing In-Reply-To: <20030304143605.3d72f6d6.jrvalverde@cnb.uam.es> Message-ID: Hi Jose What version of Jemboss/EMBOSS are you using and on what platform? I suspect this without authentication? Anyway you should find this is fixed in the currnet Jemboss release with EMBOSS-2.6.0. Regards Tim On Tue, 4 Mar 2003, Jos? R. Valverde wrote: > Hi, I'm having trouble with Jemboss concerning the hierarchihcal listing > of application menus in the top left side. This has been consistent for > quite some time, and the problem is that the listing changes each time I > start Jemboss. > > It seems like the Java application is getting an incomplete listing of > applications, truncating the list at varying points each time Jemboss is > started and offering an incomplete listing. It looks like a problem due > to a short timeout waiting for the listing of applications.. > > Anyone knows if there is a fix for this? From Wiepert.Mathieu at mayo.edu Tue Mar 4 19:17:15 2003 From: Wiepert.Mathieu at mayo.edu (Wiepert, Mathieu) Date: Tue, 4 Mar 2003 13:17:15 -0600 Subject: LINDNA Message-ID: <2F41CC6C9777D311ACBD009027B108EA0541C4FD@excsrv32.mayo.edu> Hi, I was looking at the lindna program, is there a program that can create the input files needed for this from a genbank or embl record? I saw the format needed for input, but couldn't find the program to create a file in that format, I thought seqret might do it? Thanks, -Mat From jmullersman at yahoo.com Tue Mar 4 19:43:38 2003 From: jmullersman at yahoo.com (Jerry Mullersman) Date: Tue, 4 Mar 2003 11:43:38 -0800 (PST) Subject: installation of Jemboss from EMBOSS-2.6.0 package questions Message-ID: <20030304194338.74089.qmail@web11606.mail.yahoo.com> I have been trying to install Jemboss in standalone mode from the EMBOSS-2.6.0 package on a Mandrake 9.0 i586 system. First, let me say that I can complile and install EMBOSS with no problems on this system. However, repeated attempts to install Jemboss have failed. One thing that is not very clear to me in the Jemboss intallation is the exact meaning of some of the setup prompts; I'm concerned that I may not be answering these prompts correctly and, cosequently, be causing the installation to fail. For instance, what is the meaning of "Enter java (1.3 or above) location [/usr]"? There is a "java" directory in /usr and it contains links to a jre-1.3.1_04 directory in /usr/lib. So, is it correct for me to accept the default answer /usr? Likewise, what is the meanining of "Enter EMBOSS download directory"? Does this refer to the EMBOSS-2.6.0 directory that is created by extracting the EMBOSS-2.6.0.tar file or to the directory above it? Finally, what is the best answer to "Enter where EMBOSS should be installed [/usr/local/emboss]"? In my case, the EMBOSS-2.6.0.tar file was extracted in /usr/local/emboss. My recollection is that the straight EMBOSS installation puts EMBOSS in /usr/local and its subdirectories. Wouldn't that be best for the Jemboss/EMBOSS installation, also? I haven't been able to find an explanation of these points in the available documentation, and it doesn't appear that these questions have been raised on the list during the last year (which makes me suspect that these are silly/stupid/dumb/nitwit questions). Thanks for your help. Jerry Mullersman ===== Jerald E. Mullersman, MD, PhD Associate Professor Department of Pathology East Tennessee State University PO Box 70568 Johnson City, TN 37614 phone: (423) 439-6210 fax: (423) 439-8060 From fernan at iib.unsam.edu.ar Tue Mar 4 20:55:06 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Tue, 4 Mar 2003 17:55:06 -0300 Subject: error in tfm.c Message-ID: <20030304205506.GF2971@iib.unsam.edu.ar> Hi! I have already finished the FreeBSD EMBOSS-2.6.0 port. In FreeBSD, documentation installed by third-parties goes into /usr/local/share/doc, and thus I now have all EMBOSS docs in /usr/local/share/doc/EMBOSS. This is unlike the rest of the shared data installed by EMBOSS, which goes in /usr/local/share/EMBOSS Now, I'm seeing an error when running tfm: [fernan at pi] tfm emma Displays a program's help documentation manual EMBOSS An error in tfm.c at line 63: The documentation for program 'emma' was not found. This happens with any EMBOSS program, not just with emma. This can be fixed by moving the docs to /usr/local/share/EMBOSS/doc. (In my case I created a link: cd /usr/local/share/EMBOSS/doc ln -s ../doc/EMBOSS doc) It appears then that tfm has a hard-coded reference to PREFIX/share/EMBOSS/doc to look for docs. If i want to place the docs somewhere else, where do I change this? I am no C guru but it seems to me that line 63 is not the right place. Are there other places/commands where this path is hard-coded? Now to a more general issue: is it possible to add a --docdir=DIR option to configure? Seems that there are several options to fine tune installation dirs, but not this one. Of course, then tfm (and perhaps others) should honor docdir. Right now I have to change one line in several Makefile.in files under EMBOSS-2.6.0/doc/ (using sed) to install docs in a place other than PREFIX/share/EMBOSS/doc. Though it works, it is certainly a hack (as the tfm error shows) and can be certainly managed more wisely if it can be set at configure time. Any thoughts? Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From tcarver at hgmp.mrc.ac.uk Tue Mar 4 21:03:55 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Tue, 4 Mar 2003 21:03:55 +0000 (GMT) Subject: installation of Jemboss from EMBOSS-2.6.0 package questions In-Reply-To: <20030304194338.74089.qmail@web11606.mail.yahoo.com> Message-ID: Hi Jerry, > "Enter java (1.3 or above) location [/usr]"? There is a "java" directory in > /usr and it contains links to a jre-1.3.1_04 directory in /usr/lib. So, is it > correct for me to accept the default answer /usr? I suspect you have in your path a /usr/bin/java which the script is picking up. If you type 'which java' it should tell you. I would recommend though that you get the latest J2SE 1.4.1 SDK though. > Likewise, what is the meanining of "Enter EMBOSS download directory"? This is the EMBOSS-2.6.0 directory location. It should give you this as the default in the square brackets. > Finally, what is the best answer to "Enter where > EMBOSS should be installed [/usr/local/emboss]"? In my case, the > EMBOSS-2.6.0.tar file was extracted in /usr/local/emboss. My recollection is > that the straight EMBOSS installation puts EMBOSS in /usr/local and its > subdirectories. Wouldn't that be best for the Jemboss/EMBOSS installation, > also? This is totally up to you where you want install to. I think people tend to use /usr/local/emboss if they want to keep emboss installation completely separate. Finally I would recommend a fresh download of all components (EMBOSS-2.6.0, Axis, and tomcat) when doing the installation. I hope this helps. Regards Tim Carver HGMP-RC From bioinfo at mascon.co.in Wed Mar 5 11:14:32 2003 From: bioinfo at mascon.co.in (bioinfo) Date: Wed, 5 Mar 2003 16:44:32 +0530 Subject: query Message-ID: <000801c2e308$6ddc68c0$63c809c0@bio> I need to find out if there is any module in emboss which does docking. I need to dock a fragment of a lead molecule into the active site of the target. I need to automate the whole process because i want to use the docked fragment as a startting material for generating ligands. Please tell me if there is some module that does docking so that i can incorporate it in my code. -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Wed Mar 5 11:12:41 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 05 Mar 2003 11:12:41 +0000 Subject: error in tfm.c References: <20030304205506.GF2971@iib.unsam.edu.ar> Message-ID: <3E65DBA9.5070603@ebi.ac.uk> Fernan Aguero wrote: > It appears then that tfm has a hard-coded reference to > PREFIX/share/EMBOSS/doc to look for docs. If i want to place > the docs somewhere else, where do I change this? A simple fix is to add an EMBOSS_DOCROOT variable to emboss.default I will add this for the next release. > Now to a more general issue: is it possible to add a > --docdir=DIR option to configure? Seems that there are > several options to fine tune installation dirs, but not this > one. > > Of course, then tfm (and perhaps others) should honor > docdir. If possible, we could set this as the default value. Hope this helps, Peter From jison at hgmp.mrc.ac.uk Wed Mar 5 12:03:14 2003 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Wed, 05 Mar 2003 12:03:14 +0000 Subject: query References: <000801c2e308$6ddc68c0$63c809c0@bio> Message-ID: <3E65E782.D707D2B2@hgmp.mrc.ac.uk> No, there isn't. bioinfo wrote: > I need to find out if there is any module in emboss which does > docking. I need to dock a fragment of a lead molecule into the active > site of the target. I need to automate the whole process because i > want to use the docked fragment as a startting material for generating > ligands. Please tell me if there is some module that does docking so > that i can incorporate it in my code. -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ CCP11 : http://www.hgmp.mrc.ac.uk/CCP11/ From stefanielager at fastmail.ca Wed Mar 5 14:19:46 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Wed, 5 Mar 2003 09:19:46 -0500 (EST) Subject: LINDNA Message-ID: <3E660782.00007F.82648@ns.interchange.ca> It is possible to use the EMBOSS program restrict (for positions of restriction sites), if you parse the output. Genbank and EMBL entries can probably also be parsed (using perl). But lindna (and cirdna) aren't really worth the effort, they don't produce nice graphics either. There are several plasmiddrawing programs that can draw linear maps. Stefanie > Hi, > > I was looking at the lindna program, is there a program that can > create the input files needed for this from a genbank or embl > record? I saw the format needed for input, but couldn't find the > program to create a file in that format, I thought seqret might do > it? > > Thanks, _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From ame at esbs.u-strasbg.fr Wed Mar 5 15:44:25 2003 From: ame at esbs.u-strasbg.fr (Jean-Christophe AME) Date: Wed, 5 Mar 2003 16:44:25 +0100 Subject: Mutiple alignement of blast results Message-ID: <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> Hi all, I am looking for a program (preferably for unix or Mac) that does a multiple alignment of a blast result. There used to be Mulblast (http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it doesn't seem to work anymore with the last blast outputs. Does anybody have any idea on the subject. This could be a nice and useful EMBOSS program. Thanks for any help. Jean-Christophe ________________________ Jean-Christophe Am?, PhD U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et Structurale ?cole Sup?rieure de Biotechnologie de Strasbourg P?le API Boulevard S?bastien-Brant 67400 Illkirch France tel.: 33 3 90 24 47 05 Fax.: 33 3 90 24 46 86 http://parplink.u-strasbg.fr http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 920 bytes Desc: not available URL: From lmullan at hgmp.mrc.ac.uk Wed Mar 5 15:46:33 2003 From: lmullan at hgmp.mrc.ac.uk (Lisa Mullan) Date: Wed, 5 Mar 2003 15:46:33 -0000 Subject: Mutiple alignement of blast results In-Reply-To: <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> Message-ID: You could try putting your BLAST results into http://abs.cit.nih.gov/blast/ which will covert them to fasta format, and then you can carry on with your multiple sequence alignment. Discussions abound as to who might write a BLAST wrapper or EMBOSS, but nothing has happened so far, although there are offers! HTH Lisa Mullan -----Original Message----- From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk]On Behalf Of Jean-Christophe AME Sent: Wednesday, March 05, 2003 3:44 PM To: emboss at hgmp.mrc.ac.uk Subject: Mutiple alignement of blast results Hi all, I am looking for a program (preferably for unix or Mac) that does a multiple alignment of a blast result. There used to be Mulblast (http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it doesn't seem to work anymore with the last blast outputs. Does anybody have any idea on the subject. This could be a nice and useful EMBOSS program. Thanks for any help. Jean-Christophe ________________________ Jean-Christophe Am?, PhD U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et Structurale ?cole Sup?rieure de Biotechnologie de Strasbourg P?le API Boulevard S?bastien-Brant 67400 Illkirch France tel.: 33 3 90 24 47 05 Fax.: 33 3 90 24 46 86 http://parplink.u-strasbg.fr http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From fernan at iib.unsam.edu.ar Wed Mar 5 16:44:10 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Wed, 5 Mar 2003 13:44:10 -0300 Subject: Mutiple alignement of blast results In-Reply-To: <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> References: <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> Message-ID: <20030305164410.GE12578@iib.unsam.edu.ar> +----[ Jean-Christophe AME (05.Mar.2003 12:50): | | Hi all, | I am looking for a program (preferably for unix or Mac) that does a | multiple alignment of a blast result. There used to be Mulblast | (http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it | doesn't seem to work anymore with the last blast outputs. | +----] This is exactly what blixem does: Blixem - display Blast matches as a multiple alignment. Reference: Sonnhammer ELL & Durbin R (1994). A workbench for Large Scale Sequence Homology Analysis. Comput. Applic. Biosci. 10:301-307. http://www.cgr.ki.se/cgr/groups/sonnhammer/Blixem.html Hope this helps, Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From maltsev at mcs.anl.gov Wed Mar 5 18:00:43 2003 From: maltsev at mcs.anl.gov (Natalia Maltsev) Date: Wed, 05 Mar 2003 12:00:43 -0600 Subject: Mutiple alignement of blast results In-Reply-To: References: <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> Message-ID: <5.0.2.1.0.20030305112309.0389a008@mail.mcs.anl.gov> >Hi, You can try to use our new experimental server of BlocksBlast and Phyloblocks written by our Luke Ulrich. 1. BlocksBlast: http://compbio.mcs.anl.gov/blast/psiblast_phylo.html After you'll Blast your sequence you are given an option to select sequences and submit them to Phyloblocks directly from Blast (a standalone server for PhyloBlocks is at : http://compbio.mcs.anl.gov/ulrich/phyloblock/) It will allign the sequences using Clustalw and also give you a tree from which you can create the subsets using color coding of the clustal tree. You can send selected sequence groups to BlockMaker (Henikoff's ) to create HMM profiles, concensus sequences and alignments specific to the subsets. We will very much appreciate your comments about these tools. A paper describing these tools should be out shortly Cheers, Natalia Maltsev >-----Original Message----- >From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk]On >Behalf Of Jean-Christophe AME >Sent: Wednesday, March 05, 2003 3:44 PM >To: emboss at hgmp.mrc.ac.uk >Subject: Mutiple alignement of blast results > >Hi all, >I am looking for a program (preferably for unix or Mac) that does a >multiple alignment of a blast result. There used to be Mulblast >(http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it >doesn't seem to work anymore with the last blast outputs. > >Does anybody have any idea on the subject. This could be a nice and useful >EMBOSS program. >Thanks for any help. >Jean-Christophe > > > > > >________________________ >Jean-Christophe Am?, PhD >U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et Structurale >?cole Sup?rieure de Biotechnologie de Strasbourg >P?le API >Boulevard S?bastien-Brant >67400 Illkirch >France > >tel.: 33 3 90 24 47 05 >Fax.: 33 3 90 24 46 86 > >http://parplink.u-strasbg.fr >1A1A,1A1A,FFFF>http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html Natalia Maltsev Computational Biology Group Mathematics & Computer Science Division Argonne National Laboratory 9700 S. Cass Avenue Argonne, Illinois 60439 tel. (630) 252-5195 (of.) fax (630) 252-5986 E-mail: maltsev at mcs.anl.gov From georg.otto at tuebingen.mpg.de Wed Mar 5 18:49:41 2003 From: georg.otto at tuebingen.mpg.de (Georg Wilhelm Otto) Date: Wed, 5 Mar 2003 19:49:41 +0100 Subject: Mutiple alignement of blast results In-Reply-To: <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> Message-ID: <3959213E-4F3B-11D7-A36B-003065C99468@tuebingen.mpg.de> Hi Jean-Christoph, I usually do this in two steps: First i filter and align my blast results using MSPcrunch (see http://www.cgr.ki.se/cgr/groups/sonnhammer/MSPcrunch.html), then i visualize the result using BLIXEM (see http://www.cgr.ki.se/cgr/groups/sonnhammer/Blixem.html). hope that helps, georg On Wednesday, March 5, 2003, at 04:44 PM, Jean-Christophe AME wrote: > Hi all, > I am looking for a program (preferably for unix or Mac) that does a > multiple alignment of a blast result. There used to be Mulblast > (http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it > doesn't seem to work anymore with the last blast outputs. > > Does anybody have any idea on the subject. This could be a nice and > useful EMBOSS program. > Thanks for any help. > Jean-Christophe > > > > ________________________ > Jean-Christophe Am?, PhD > U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et > Structurale > ?cole Sup?rieure de Biotechnologie de Strasbourg > P?le API > Boulevard S?bastien-Brant > 67400 Illkirch > France > > tel.: 33 3 90 24 47 05 > Fax.: 33 3 90 24 46 86 > > http://parplink.u-strasbg.fr > http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1322 bytes Desc: not available URL: From georg.otto at tuebingen.mpg.de Wed Mar 5 19:04:10 2003 From: georg.otto at tuebingen.mpg.de (Georg Wilhelm Otto) Date: Wed, 5 Mar 2003 20:04:10 +0100 Subject: Primer design Message-ID: <3F14B12D-4F3D-11D7-A36B-003065C99468@tuebingen.mpg.de> Hi all! I have a problem concerning PCR primer design. I have a lot of sequences of very different length and I want to design PCR primers to all of them within a given maximum distance from the 3-prime end - say 500 bp. I don't want to have to look at all the sequences because it is a lot. Primer3 does not seem to support this, it lets you only define ranges from the 5-prime end. Does anyone know how it could be done in Primer3 or how it could be done using another primer design software? Of course there is the obvious solution to revert the sequences and then define the distance from the 5-prime end, but i don't want to do this. Thanks a lot! Georg -- Georg Wilhelm Otto Max-Planck-Institute for Developmental Biology Spemannstrasse 35/III D-72076 Tuebingen Germany phone: +49 7071 601 301 http://www.eb.tuebingen.mpg.de From yezq at mail.cbi.pku.edu.cn Thu Mar 6 09:32:55 2003 From: yezq at mail.cbi.pku.edu.cn (Zhiqiang Ye) Date: Thu, 6 Mar 2003 17:32:55 +0800 Subject: single program complilaiton Message-ID: <200303060906.h2696Jj23619@mail.cbi.pku.edu.cn> Dear Sir/Madam? I want to use only one(e.g. needle) or just several programs in EMBOSS package. Can I just compile these several programs , not the whole EMBOSS package? Thanks in advance! ???????? Best Regards! ??????????????Zhiqiang Ye ?????????????????2003-03-06 From letondal at pasteur.fr Thu Mar 6 14:16:48 2003 From: letondal at pasteur.fr (Catherine Letondal) Date: Thu, 06 Mar 2003 15:16:48 +0100 Subject: Mutiple alignement of blast results In-Reply-To: Your message of "Wed, 05 Mar 2003 16:44:25 +0100." <578F1C5E-4F21-11D7-89EC-0005024329A7@esbs.u-strasbg.fr> Message-ID: <200303061416.h26EGnDS435024@electre.pasteur.fr> Jean-Christophe AME wrote: > Hi all, > I am looking for a program (preferably for unix or Mac) that does a=20 > multiple alignment of a blast result. There used to be Mulblast=20 > (http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it=20 > doesn't seem to work anymore with the last blast outputs. > > Does anybody have any idea on the subject. This could be a nice and=20 > useful EMBOSS program. > Thanks for any help. > Jean-Christophe > Hi Jean-Christophe, Just in case you don't have enough tools suggestion... : See, at: http://bioweb.pasteur.fr/seqanal/blast/intro-uk.html Blast post-processing: MSPcrunch MVIEW html4blast seqsblast (extraction of sequences from a Blast output) (alignment, then phylogenetic tools are then available on extracted sequences) -- Catherine Letondal -- Pasteur Institute Computing Center From rls at ebi.ac.uk Thu Mar 6 14:41:05 2003 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Thu, 6 Mar 2003 14:41:05 -0000 Subject: Mutiple alignement of blast results In-Reply-To: <200303061416.h26EGnDS435024@electre.pasteur.fr> Message-ID: Hi, Also, please take into consideration dbclustal which does what you need. You can see it working oif you run a wu-blast at the EBI against swall. Once the job is completed, click on Run dbclustal and choose which matches you wish to align. The reference to dbclustal is: "Rapid and reliable global multiple alignments of protein sequences detected by database searches" Thompson J.D., Plewnial F., Thierry J.-C. and Poch O. Nucleic Acid Research, 2000, Vol.28, No 15 2919-2926 R:) > -----Original Message----- > From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk]On > Behalf Of Catherine Letondal > Sent: 06 March 2003 14:17 > To: Jean-Christophe AME > Cc: emboss at hgmp.mrc.ac.uk > Subject: Re: Mutiple alignement of blast results > > > > Jean-Christophe AME wrote: > > Hi all, > > I am looking for a program (preferably for unix or Mac) that does a=20 > > multiple alignment of a blast result. There used to be Mulblast=20 > > (http://www.cbs.cnrs.fr/Soft_ModMol/MulBlast/MulBlast-en.html) but it=20 > > doesn't seem to work anymore with the last blast outputs. > > > > Does anybody have any idea on the subject. This could be a nice and=20 > > useful EMBOSS program. > > Thanks for any help. > > Jean-Christophe > > > > Hi Jean-Christophe, > > Just in case you don't have enough tools suggestion... : > See, at: http://bioweb.pasteur.fr/seqanal/blast/intro-uk.html > Blast post-processing: > MSPcrunch > MVIEW > html4blast > seqsblast (extraction of sequences from a Blast output) > (alignment, then phylogenetic tools are then > available on extracted > sequences) > > -- > Catherine Letondal -- Pasteur Institute Computing Center > From d.m.a.martin at dundee.ac.uk Thu Mar 6 14:57:21 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 06 Mar 2003 14:57:21 +0000 Subject: Getting database sizes for indexed databases Message-ID: Is there an easy way to determine the size (ie number of sequences) in a database? Could such information be added to showdb? I realise that in many cases this will be very difficult/impossible to determine. I am thinking of emblcd indexed databases. It must be possible to count the number of sequences in each file indexed and then use the file: wild cards to build a total for that database. regards ..d -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From pmr at ebi.ac.uk Thu Mar 6 15:13:18 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 06 Mar 2003 15:13:18 +0000 Subject: Getting database sizes for indexed databases References: Message-ID: <3E67658E.2080309@ebi.ac.uk> David Martin wrote: > Is there an easy way to determine the size (ie number of sequences) in a > database? > Could such information be added to showdb? > > I am thinking of emblcd indexed databases. It must be possible to count the > number of sequences in each file indexed and then use the file: wild cards > to build a total for that database. For EMBLCD databases it can be read from the index files (the number is in the header). For SRS databases a simple query can return the count. For complex cases there may be no answer - but we can either write a short message, or add an attribute to the database definition in emboss.default. So ... is this a useful addition to showdb? Peter From gwilliam at hgmp.mrc.ac.uk Thu Mar 6 15:22:09 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 06 Mar 2003 15:22:09 +0000 Subject: Getting database sizes for indexed databases References: <3E67658E.2080309@ebi.ac.uk> Message-ID: <3E6767A0.B906E106@hgmp.mrc.ac.uk> Or should it be reported by a seprarate program? Peter Rice wrote: > > So ... is this a useful addition to showdb? > > Peter -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From d.m.a.martin at dundee.ac.uk Thu Mar 6 15:24:34 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 06 Mar 2003 15:24:34 +0000 Subject: Getting database sizes for indexed databases In-Reply-To: <3E67658E.2080309@ebi.ac.uk> Message-ID: On 6/3/03 3:13 pm, "Peter Rice" wrote: > David Martin wrote: >> Is there an easy way to determine the size (ie number of sequences) in a >> database? >> Could such information be added to showdb? >> >> I am thinking of emblcd indexed databases. It must be possible to count the >> number of sequences in each file indexed and then use the file: wild cards >> to build a total for that database. > > For EMBLCD databases it can be read from the index files (the number is > in the header). It can if the database definition matches the files indexed. eg I have swiss, trembl and trembl_new all indexed together as sptr. I use the same index files for sw (swiss only) and trembl (trembl+trembl_new) The index file will give the total for all three or the total for each file? If it is the total for each file then the true count for subdivisions of the database can be found by matching the file: definition to the list of files int he header. If it is the global total then there is no direct way of determining the database size without specifically capturing that with the indexing program. What is the header format for the index files? ..d > > For SRS databases a simple query can return the count. > > For complex cases there may be no answer - but we can either write a > short message, or add an attribute to the database definition in > emboss.default. > > So ... is this a useful addition to showdb? > > Peter > > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From jrvalverde at cnb.uam.es Thu Mar 6 15:44:44 2003 From: jrvalverde at cnb.uam.es (José R. Valverde) Date: Thu, 6 Mar 2003 16:44:44 +0100 Subject: Getting database sizes for indexed databases In-Reply-To: References: Message-ID: <20030306164444.537c8216.jrvalverde@cnb.uam.es> On Thu, 06 Mar 2003 14:57:21 +0000 David Martin wrote: > > Is there an easy way to determine the size (ie number of sequences) in a > database? > Could such information be added to showdb? > The easy way: grep $entry database May not give you what you want if you refer not to records but entry numbers. Ah, but then this happens in databases like embl and swissprot.. The even easier way: See the README file which contains the number of entries. j From d.m.a.martin at dundee.ac.uk Thu Mar 6 17:04:55 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 06 Mar 2003 17:04:55 +0000 Subject: problems with indexing refseq Message-ID: I am getting strange behaviour with refseq. When indexing the genbank format cumulative files (rscu.gbff) with dbiflat -idformat GB I get an index that returns the wrong sequences. eg attempting to retrieve NM_060207 instead retrieves NM_131801 which is a totally different sequence entry. Attempting to retrieve NM131801 gives NM_165909. Any thoughts on how to debug this effect. entret -debug indicates that the right entry is found in the index but the entry read is incorrect. ..d -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From squiresb at macrogenics.com Wed Mar 12 04:03:54 2003 From: squiresb at macrogenics.com (Burke Squires) Date: Tue, 11 Mar 2003 22:03:54 -0600 Subject: I have an accession number, can I extract genbank information from an on-line database? Message-ID: Hello EMBOSSers, Is it possible to extract genbank file information from an on-line database if I have an accession number or do I have to download the hundreds of genbank files locally and extract it from that? If so how? I have read information on seqret and it seems truly wonderful but it seems to work only with local databases? Thanks! Burke Squires -- Burke Squires Bioinformatics MacroGenics, Inc. Dallas, TX From David.Bauer at SCHERING.DE Wed Mar 12 06:42:30 2003 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Wed, 12 Mar 2003 07:42:30 +0100 Subject: I have an accession number, can I extract genbank information from an on-line database? Message-ID: (See attached file: C.htm) -------------- next part -------------- An HTML attachment was scrubbed... URL: From hkawai at venus.dti.ne.jp Wed Mar 12 11:13:13 2003 From: hkawai at venus.dti.ne.jp (Hironori Kawai) Date: Wed, 12 Mar 2003 20:13:13 +0900 Subject: problems with indexing refseq In-Reply-To: References: Message-ID: <200303121111.h2CBBrME027328@smtp4.dti.ne.jp> Hello David Martin wrote: > I am getting strange behaviour with refseq. > > When indexing the genbank format cumulative files (rscu.gbff) with dbiflat > -idformat GB I get an index that returns the wrong sequences. > > eg attempting to retrieve NM_060207 instead retrieves NM_131801 which is a > totally different sequence entry. > Attempting to retrieve NM131801 gives NM_165909. This problem was described in this ML. If you are using version 2.5.0 or earlier (I guess you do so), I recommend to update this to 2.5.1 or later. In addition, you have to reformat rscu.gbff file in the way that the word following LOCUS in each entry is replaced to their Accession No. In this ML, a perl script which reformats in such way, are uploaded (the Message-ID <2DC41140A89ED411989D00508BDCD9ED01E28754@ bi-exsrv1.iapc.bbsrc.ac.uk>). Hironori Kawai From siegmund at develogen.com Wed Mar 12 11:28:25 2003 From: siegmund at develogen.com (Thomas Siegmund) Date: Wed, 12 Mar 2003 12:28:25 +0100 Subject: I have an accession number, can I extract genbank information from an on-line database? In-Reply-To: References: Message-ID: <200303121228.25817.siegmund@develogen.com> Hi Burke, if you have blast databases in house, you can use fastacmd (comes with blast) to extract single sequences in fasta format from the binary database. With a emboss.default like this you can access the blast database in EMBOSS: DB nt [ methodentry: app app: "fastacmd -d/data/blast/data/nt -s%s" type: N format: fasta comment: "nt - non redundant nucleotide sequences" ] Regards Thomas Am Mittwoch, 12. M?rz 2003 05:03 schrieb Burke Squires: > Hello EMBOSSers, > > Is it possible to extract genbank file information from an on-line database > if I have an accession number or do I have to download the hundreds of > genbank files locally and extract it from that? If so how? I have read > information on seqret and it seems truly wonderful but it seems to work > only with local databases? > > Thanks! > > Burke Squires -- Thomas Siegmund, Ph.D. DeveloGen AG Bioinformatics and Data Management Phone: +49(551) 505 58 651 From jison at hgmp.mrc.ac.uk Wed Mar 12 13:42:37 2003 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Wed, 12 Mar 2003 13:42:37 +0000 Subject: EMBOSS Programming Course Message-ID: <3E6F394D.E4C4830B@hgmp.mrc.ac.uk> Hi Details on a forthcoming FREE programming course for bioinformatics using EMBOSS are below. Apologies if not interested. Please forward to anyone you think might be interested. Cheers Jon Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk BSDC 2003 Bioinformatics Software Development Courses May 13-15, June 17-19, Sep 16-18 2003 A course on 'Bioinformatics Software Development' using EMBOSS will be held in the training room at Hinxton Hall on May 13-15, June 17-19 and Sep 16-18 2003. The course will give a good introduction to programming in EMBOSS. By the end of the course you will be experienced in all the steps in writing a basic bioinformatics application using the EMBOSS programming libraries. The course would suit competent programmers, probably with at least a couple of years of experience. A reasonable working knowledge of C is required, familiarity with pointers is helpful but not essential. The three dates are likely to get booked up very quickly so please email Karen Hampson (khampson at hgmp.mrc.ac.uk) to register as soon as possible. To read more about EMBOSS see EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ From Johanne.Duhaime at ircm.qc.ca Wed Mar 12 21:29:17 2003 From: Johanne.Duhaime at ircm.qc.ca (Duhaime Johanne) Date: Wed, 12 Mar 2003 16:29:17 -0500 Subject: Seqret does not work in a crontab Message-ID: <75CDD43E62D698448ED86E23C290A2760A2B90@pandore.ircm.priv> Hello I have a perl program that use "seqret" to retrieve a list of sequences (and do other things). The target command used is: seqret -sequence=@/seqdata/seqdatabases/protein_embl/mammalian/mammalian.id -outseq=/seqdata/seqdatabases/protein_embl/mammalian/mammalian.dat -osformat=SWISS The file /seqdata/seqdatabases/protein_embl/mammalian/mammalian.id contains names of sequenes like: prot:143B_BOVIN prot:143B_HUMAN prot:143B_MOUSE (...) and prot is define in .embossrc This program works fine on the command line call. The problem arises when I put that program in a crontab. Then I have the following: Reads and writes (returns) sequences Error: failed to open filename prot Error: Unable to read sequence '@/seqdata/seqdatabases/protein_embl/mammalian/mammalian.id' erreur : It looks like it could recognize "prot". Can you help me? From squiresb at macrogenics.com Thu Mar 13 01:43:49 2003 From: squiresb at macrogenics.com (Burke Squires) Date: Wed, 12 Mar 2003 19:43:49 -0600 Subject: Accessing online databases... In-Reply-To: Message-ID: Hello, Thanks for your help! If I could ask another questions...I checked out the admin?s guide and I found the following information: DB mydb [ # required parameters method: url format: genbank url: "http://www.infobiogen.fr/srs5bin/cgi-bin/wgetz?-e+[genbank-id:%s]" #optional parameters type: N comment: "Genbank by ID from InfoBiogen" ] I have also found and pasted this into my emboss.default.template. What do I need to do to get this to show up in ?showdb?? Any information or URL?s to accessing an online database using a Genbank accession number would be greatly appreciated! Thanks! Burke -- Burke Squires Bioinformatics MacroGenics, Inc. 2600 Stemmons Freeway, Suite 210 Dallas, TX 75235 USA Work: 214-634-3000 X224 Fax: 214-634-3002 ---------------------------------------------------------------------------- This e-mail and any attachments may be confidential or legally privileged. If you received this message in error or are not the intended recipient, you should destroy the e-mail message and any attachments or copies, and you are prohibited from retaining, distributing, disclosing or using any information contained herein. Please inform us of the erroneous delivery by return e-mail. Thank you for your cooperation. > > From: David.Bauer at SCHERING.DE > Date: Wed, 12 Mar 2003 07:42:30 +0100 > To: squiresb at macrogenics.com > Cc: emboss at embnet.org > Subject: Re: I have an accession number, can I extract genbank information > from an on-line database? > > > > (See attached file: C.htm) -------------- next part -------------- An HTML attachment was scrubbed... URL: From ableasby at hgmp.mrc.ac.uk Thu Mar 13 10:31:09 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 13 Mar 2003 10:31:09 GMT Subject: Accessing online databases... Message-ID: <200303131031.h2DAV9V16580@bromine.hgmp.mrc.ac.uk> Burke, You need to rename emboss.default.template to emboss.default. The URL given in the admin guide is out of date. You'll have to replace your entry with something like: DB mydb [ # required parameters method: url format: genbank url: "http://www.infobiogen.fr/srs7bin/cgi-bin/wgetz?-e+-ascii+[genbank-id:%s]" #optional parameters type: N comment: "Genbank by ID from InfoBiogen" ] HTH Alan Bleasby HGMP From Wiepert.Mathieu at mayo.edu Thu Mar 13 12:57:25 2003 From: Wiepert.Mathieu at mayo.edu (Wiepert, Mathieu) Date: Thu, 13 Mar 2003 06:57:25 -0600 Subject: est2genome output to genbank format? Message-ID: <2F41CC6C9777D311ACBD009027B108EA0541C558@excsrv32.mayo.edu> Hi, Is it possible to have est2genome give output in genbank format (or ensembl), with exons and introns annotated as features on the genome sequence? OR is there something that can take the output and parse it into that format? Description of the tool notes that " This format is easy to parse into other software. " wondered if someone had come up with a handy widget to do something like this, or if it was already available. Thanks, -Mat From jason at cgt.mc.duke.edu Thu Mar 13 14:00:50 2003 From: jason at cgt.mc.duke.edu (Jason Stajich) Date: Thu, 13 Mar 2003 09:00:50 -0500 (EST) Subject: est2genome output to genbank format? In-Reply-To: <2F41CC6C9777D311ACBD009027B108EA0541C558@excsrv32.mayo.edu> References: <2F41CC6C9777D311ACBD009027B108EA0541C558@excsrv32.mayo.edu> Message-ID: Mat - Bio::Tools::Est2Genome ... Although it doesn't construct proper genes as I would like. -jason On Thu, 13 Mar 2003, Wiepert, Mathieu wrote: > Hi, > > Is it possible to have est2genome give output in genbank format (or ensembl), with exons and introns annotated as features on the genome sequence? OR is there something that can take the output and parse it into that format? Description of the tool notes that " This format is easy to parse into other software. " wondered if someone had come up with a handy widget to do something like this, or if it was already available. > > Thanks, > > -Mat > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From pmr at ebi.ac.uk Thu Mar 13 14:14:54 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 13 Mar 2003 14:14:54 +0000 Subject: est2genome output to genbank format? References: <2F41CC6C9777D311ACBD009027B108EA0541C558@excsrv32.mayo.edu> Message-ID: <3E70925E.9080009@ebi.ac.uk> Wiepert, Mathieu wrote: > Is it possible to have est2genome give output in genbank format (or ensembl), > with exons and introns annotated as features on the genome sequence? Soon ... EMBOSS reports can be written as GFF or EMBL feature tables. All you need is a change to est2genome to write an EMBOSS report. The main reason est2genome has not been converted yet is the need to also write an alignment report and to preserve the original format for users who already parse it into something else. High on the list of things to do ... especially now someone has asked for it :-) Expect something in the next couple of months. As for other parsers for est2genome .... there are parsers at the Sanger Institute for their annotation pipelines. You could try contacting them for help and advice. regards, Peter Rice From battaile at mcw.edu Thu Mar 13 15:33:23 2003 From: battaile at mcw.edu (Kevin Battaile) Date: Thu, 13 Mar 2003 09:33:23 -0600 (CST) Subject: jemboss installation question Message-ID: <38634.141.106.116.74.1047569603.squirrel@post.its.mcw.edu> I have been trying to install jemboss in client-server mode on a redhat linux box (7.3 and 8.0) without much success. I can get the standalone version working on the 8.0 box (haven't tried on the 7.3 box) but the trouble seems to start when I want to go client-server. I have the following distributions: EMBOSS-2.6.0 j2sdk1.4.0_01 jakarta-tomcat-4.0.4 xml-axis-10 I run the install-jemboss-server.sh script as myself, and I also own the jakarta and xml-axis directories. Everything seems to go fine during the installation. Tomstart appears to start tomcat as I can get the tomcat web page saying it is installed. When I run runJemboss.csh, I get a bunch of error messages spewing out on the terminal window. I login using my linux username and password and when I try to run anything I get a window that says there is a problem connecting to the server. I pasted a portion of the error messages below. Does anyone have any idea what I could be doing wrong? I like the standalone interface and would like to get the client-server version working so the people in our group can use it from their pc. Thanks, Kevin ======================================= [battaile at linux3 jemboss]$ ./runJemboss.csh [1] 4093 [battaile at linux3 jemboss]$ Warning: Cannot convert string "Escape,_Key_Cancel" to type VirtualBinding Warning: Cannot convert string "Home,_Key_Begin" to type VirtualBinding Warning: Cannot convert string "F1,_Key_Help" to type VirtualBinding Warning: Cannot convert string "ShiftF10,_Key_Menu" to type VirtualBinding Warning: Cannot convert string "F10,Shift_Key_Menu" to type VirtualBinding Warning: Cannot convert string "KP_Enter,_Key_Execute" to type VirtualBinding Warning: Cannot convert string "AltReturn,Alt_Key_KP_Enter" to type VirtualBinding calling the server Mar 13, 2003 9:16:57 AM org.apache.axis.client.Call invoke INFO: Mapping Exception to AxisFault AxisFault faultCode: {http://xml.apache.org/axis/}Server.userException faultString: java.lang.NullPointerException faultActor: null faultDetail: stackTrace: java.lang.NullPointerException at org.emboss.jemboss.programs.RunEmbossApplication.isProcessStdout(RunEmbossApplication.java:71) at org.emboss.jemboss.server.JembossAuthServer.show_db(JembossAuthServer.java:326) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:324) at org.apache.axis.providers.java.RPCProvider.invokeMethod(RPCProvider.java:372) at org.apache.axis.providers.java.RPCProvider.processMessage(RPCProvider.java:292) at org.apache.axis.providers.java.JavaProvider.invoke(JavaProvider.java:276) at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:71) at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:156) at org.apache.axis.SimpleChain.invoke(SimpleChain.java:126) at org.apache.axis.handlers.soap.SOAPService.invoke(SOAPService.java:437) at org.apache.axis.server.AxisServer.invoke(AxisServer.java:316) at org.apache.axis.transport.http.AxisServlet.doPost(AxisServlet.java:701) at javax.servlet.http.HttpServlet.service(HttpServlet.java:760) at org.apache.axis.transport.http.AxisServletBase.service(AxisServletBase.java:335) at javax.servlet.http.HttpServlet.service(HttpServlet.java:853) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:247) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:243) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:190) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566) at org.apache.catalina.valves.CertificatesValve.invoke(CertificatesValve.java:246) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943) at org.apache.catalina.core.StandardContext.invoke(StandardContext.java:2347) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:180) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566) at org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherValve.java:170) From david at cnb.uam.es Thu Mar 13 16:10:06 2003 From: david at cnb.uam.es (David Garcia Aristegui) Date: Thu, 13 Mar 2003 17:10:06 +0100 Subject: jemboss installation question In-Reply-To: <38634.141.106.116.74.1047569603.squirrel@post.its.mcw.edu> References: <38634.141.106.116.74.1047569603.squirrel@post.its.mcw.edu> Message-ID: Don?t worry about the firsts warnings ( is a common problem with the java interface an the Red Hat, for example ). About the java errors: it seems you have a problem with the Tomcat or the Axis/SOAP installation. - Tomcat is runnig for sure? you can execute properly the examples from your own tomcat installation? - Look at the catalina.out logs under the tomcat installation, it gives you lot of information; look what is the port reserved for tomcat, other process are runnig on the same port?. - If you have to run again the install script: check out the java environment variable. - Install script: "The script asks for the locations of the EMBOSS download, EMBOSS installation, Tomcat, Axis and Java directories. Axis is added to the Tomcat (copying soap.war to $TOMCAT/webapps/ )." Copy the soap.war again... and restart. "The Jemboss server classes are added to the Tomcat CLASSPATH ($TOMCAT/webapps/axis/WEB-INF/classes/)". Look at the classes directory, and check the symbolic links, they are pointing the correct files? Maybe is a path problem. - Check out the jemboss.properties file under $EMBOSS_ROOT/share/EMBOSS/jemboss/resource/jemboss.properties. Hope this helps, and excuse me, my english is terrible. David. >I have been trying to install jemboss in client-server mode on a redhat >linux box (7.3 and 8.0) without much success. I can get the standalone >version working on the 8.0 box (haven't tried on the 7.3 box) but the >trouble seems to start when I want to go client-server. > >I have the following distributions: >EMBOSS-2.6.0 >j2sdk1.4.0_01 >jakarta-tomcat-4.0.4 >xml-axis-10 > >I run the install-jemboss-server.sh script as myself, and I also own the >jakarta and xml-axis directories. Everything seems to go fine during the >installation. Tomstart appears to start tomcat as I can get the tomcat web >page saying it is installed. When I run runJemboss.csh, I get a bunch of >error messages spewing out on the terminal window. I login using my linux >username and password and when I try to run anything I get a window that >says there is a problem connecting to the server. I pasted a portion of >the error messages below. > >Does anyone have any idea what I could be doing wrong? I like the >standalone interface and would like to get the client-server version >working so the people in our group can use it from their pc. > >Thanks, > >Kevin > >======================================= > >[battaile at linux3 jemboss]$ ./runJemboss.csh >[1] 4093 >[battaile at linux3 jemboss]$ Warning: Cannot convert string >"Escape,_Key_Cancel" to type VirtualBinding >Warning: Cannot convert string "Home,_Key_Begin" to type VirtualBinding >Warning: Cannot convert string "F1,_Key_Help" to type VirtualBinding >Warning: Cannot convert string "ShiftF10,_Key_Menu" to type >VirtualBinding >Warning: Cannot convert string "F10,Shift_Key_Menu" to type >VirtualBinding >Warning: Cannot convert string "KP_Enter,_Key_Execute" to type >VirtualBinding >Warning: Cannot convert string "AltReturn,Alt_Key_KP_Enter" to type >VirtualBinding >calling the server >Mar 13, 2003 9:16:57 AM org.apache.axis.client.Call invoke >INFO: Mapping Exception to AxisFault >AxisFault > faultCode: {http://xml.apache.org/axis/}Server.userException > faultString: java.lang.NullPointerException > faultActor: null > faultDetail: > stackTrace: java.lang.NullPointerException > at >org.emboss.jemboss.programs.RunEmbossApplication.isProcessStdout(RunEmbossApplication.java:71) > at >org.emboss.jemboss.server.JembossAuthServer.show_db(JembossAuthServer.java:326) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at >sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at >sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:324) > at >org.apache.axis.providers.java.RPCProvider.invokeMethod(RPCProvider.java:372) > at >org.apache.axis.providers.java.RPCProvider.processMessage(RPCProvider.java:292) > at >org.apache.axis.providers.java.JavaProvider.invoke(JavaProvider.java:276) > at >org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:71) > at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:156) > at org.apache.axis.SimpleChain.invoke(SimpleChain.java:126) > at >org.apache.axis.handlers.soap.SOAPService.invoke(SOAPService.java:437) > at org.apache.axis.server.AxisServer.invoke(AxisServer.java:316) > at >org.apache.axis.transport.http.AxisServlet.doPost(AxisServlet.java:701) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:760) > at >org.apache.axis.transport.http.AxisServletBase.service(AxisServletBase.java:335) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:853) > at >org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:247) > at >org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:193) > at >org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:243) > at >org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566) > at >org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472) > at >org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943) > at >org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:190) > at >org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566) > at >org.apache.catalina.valves.CertificatesValve.invoke(CertificatesValve.java:246) > at >org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564) > at >org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472) > at >org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943) > at >org.apache.catalina.core.StandardContext.invoke(StandardContext.java:2347) > at >org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:180) > at >org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566) > at >org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherValve.java:170) -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jack.Leunissen at wur.nl Thu Mar 13 22:54:54 2003 From: Jack.Leunissen at wur.nl (Jack Leunissen) Date: Thu, 13 Mar 2003 23:54:54 +0100 Subject: Accessing online databases... In-Reply-To: <200303131031.h2DAV9V16580@bromine.hgmp.mrc.ac.uk> Message-ID: <006701c2e9b3$904d2d70$0300000a@kuifje> Also note the change from SRS5 to SRS7. Version 5 is out of date by several years. I guess that manual needs some cleaning up... Cheers, Jack Jack A.M. Leunissen Genome Informatics Wageningen University 6703 HA Wageningen, NL > -----Original Message----- > From: owner-emboss at hgmp.mrc.ac.uk > [mailto:owner-emboss at hgmp.mrc.ac.uk] On Behalf Of > ableasby at hgmp.mrc.ac.uk > Sent: Thursday, 13 March, 2003 11:31 > To: emboss at hgmp.mrc.ac.uk; squiresb at macrogenics.com > Subject: Re: Accessing online databases... > > > Burke, > > You need to rename emboss.default.template to emboss.default. > > The URL given in the admin guide is out of date. You'll > have to replace your entry with something like: > > DB mydb [ > # required parameters > method: url > format: genbank > url: > "http://www.infobiogen.fr/srs7bin/cgi-bin/wgetz?-e+-ascii+[gen bank-id:%s]" #optional parameters type: N comment: "Genbank by ID from InfoBiogen" ] HTH Alan Bleasby HGMP From kellert at ohsu.edu Thu Mar 13 22:58:48 2003 From: kellert at ohsu.edu (Thomas Keller) Date: Thu, 13 Mar 2003 14:58:48 -0800 Subject: tempdata availability Message-ID: <59C9956D-55A7-11D7-AAF0-0003930405E2@ohsu.edu> Greetings, I must be missing something obvious. I know eprimer3 is working, I've used it with my own datafiles. But when I try to use the test databases I get the following: kellert% eprimer3 tembl:hsfau1 hsfau.eprimer3 -explain Picks PCR primers and hybridization oligos Warning: Cannot open division file '' for database 'tembl' Warning: seqCdQry failed Error: Unable to read sequence 'tembl:hsfau1' ########################### My embossdata output follows, but I thought emboss.default would be used to look in /my_emboss_path/EMBOSS/test for the test dbs. I have set my_emboss_path in emboss.defaults. kellert% embossdata Finds or fetches the data files read in by the EMBOSS programs # The following directories can contain EMBOSS data files. # They are searched in the following order until the file is found. # If the directory does not exist, then this is noted below. # '.' is the UNIX name for your current working directory. . Exists .embossdata Does not exist /Users/kellert Exists /Users/kellert/.embossdata Does not exist /usr/local/biotools/share/EMBOSS/data/ Exists ################# Thanks for your help, Tom Thomas J. Keller, Ph.D. Director, MMI Core Facility Oregon Health & Science University 3181 SW Sam Jackson Park Rd. Portland, OR, USA, 97239 http://www.ohsu.edu/core From d.m.a.martin at dundee.ac.uk Thu Mar 13 23:41:14 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 13 Mar 2003 23:41:14 +0000 Subject: Accessing online databases... In-Reply-To: <006701c2e9b3$904d2d70$0300000a@kuifje> Message-ID: On 13/3/03 10:54 pm, "Jack Leunissen" wrote: > Also note the change from SRS5 to SRS7. Version 5 is out of date > by several years. I guess that manual needs some cleaning up... There have been a lot of changes since I last updated it. Someone else had offered to update it with th elatest developments as I have not had the time. ..d > > Cheers, > Jack > > > > Jack A.M. Leunissen > Genome Informatics > Wageningen University > 6703 HA Wageningen, NL > > > >> -----Original Message----- >> From: owner-emboss at hgmp.mrc.ac.uk >> [mailto:owner-emboss at hgmp.mrc.ac.uk] On Behalf Of >> ableasby at hgmp.mrc.ac.uk >> Sent: Thursday, 13 March, 2003 11:31 >> To: emboss at hgmp.mrc.ac.uk; squiresb at macrogenics.com >> Subject: Re: Accessing online databases... >> >> >> Burke, >> >> You need to rename emboss.default.template to emboss.default. >> >> The URL given in the admin guide is out of date. You'll >> have to replace your entry with something like: >> >> DB mydb [ >> # required parameters >> method: url >> format: genbank >> url: >> "http://www.infobiogen.fr/srs7bin/cgi-bin/wgetz?-e+-ascii+[gen > bank-id:%s]" > #optional parameters > type: N > comment: "Genbank by ID from InfoBiogen" > ] > > > HTH > > Alan Bleasby > HGMP > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From Johanne.Duhaime at ircm.qc.ca Fri Mar 14 20:14:59 2003 From: Johanne.Duhaime at ircm.qc.ca (Duhaime Johanne) Date: Fri, 14 Mar 2003 15:14:59 -0500 Subject: TR: Seqret does not work in a crontab Message-ID: <75CDD43E62D698448ED86E23C290A2760A3783@pandore.ircm.priv> Thank you everyone for answers. The problem was solved by putting .embossrc in the $HOME of the user. ------ I have a perl program that use "seqret" to retrieve a list of sequences (and do other things). The target command used is: seqret -sequence=@/seqdata/seqdatabases/protein_embl/mammalian/mammalian.id -outseq=/seqdata/seqdatabases/protein_embl/mammalian/mammalian.dat -osformat=SWISS The file /seqdata/seqdatabases/protein_embl/mammalian/mammalian.id contains names of sequenes like: prot:143B_BOVIN prot:143B_HUMAN prot:143B_MOUSE (...) and prot is define in .embossrc This program works fine on the command line call. The problem arises when I put that program in a crontab. Then I have the following: Reads and writes (returns) sequences Error: failed to open filename prot Error: Unable to read sequence '@/seqdata/seqdatabases/protein_embl/mammalian/mammalian.id' erreur : It looks like it could recognize "prot". Can you help me? From davids at synpep.com Fri Mar 14 22:26:59 2003 From: davids at synpep.com (David Stephens) Date: Fri, 14 Mar 2003 14:26:59 -0800 Subject: How to Save Time, Resources and Expenses by Outsourcing Peptide Synthesis Message-ID: <20030314223432.4EE737D256@mercury.hgmp.mrc.ac.uk> An HTML attachment was scrubbed... URL: From tomembers at premiumsmail.net Sun Mar 16 09:39:23 2003 From: tomembers at premiumsmail.net (Reunion.com) Date: Sun, 16 Mar 2003 01:39:23 -0800 Subject: Is Your High School Sweetheart Single? Message-ID: <20030316094938.19CC17D0DE@mercury.hgmp.mrc.ac.uk> WHERE IS YOUR HIGH SCHOOL SWEETHEART NOW? Find out by joining Reunion.com today. Access your High School class list, emails, message boards and photos or find out if your old Prom Queen is still single! 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Please contact PremiumsMail for any comments you may have regarding your participation. We may transfer your e-mail address to our partners at any time. *********************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From xbizoy01 at yahoo.fr Mon Mar 17 08:22:55 2003 From: xbizoy01 at yahoo.fr (=?iso-8859-1?q?yann=20bizouerne?=) Date: Mon, 17 Mar 2003 09:22:55 +0100 (CET) Subject: Index EMBL and EMBLnew Message-ID: <20030317082255.68285.qmail@web20803.mail.yahoo.com> I want to work with EMBL and EMBLnew. I have index the EMBL files and the EMBL new filers in separate directories.(/EMBL/ & /EMBLnew/). I did this because I just want to re-index EMBLnew when new sequences are coming, and not all the sequences (EMBL + EMBLnew) Now I want to interogate againts these two databases with one request. How could I do such thing ? Is it the good way to work with EMBL or not ? Thanks in advance for your help. Yann BIZOUERNE --------------------------------- Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en fran?ais ! Testez le nouveau Yahoo! Mail -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Mon Mar 17 10:46:25 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 17 Mar 2003 10:46:25 +0000 Subject: Index EMBL and EMBLnew References: <20030317082255.68285.qmail@web20803.mail.yahoo.com> Message-ID: <3E75A781.4060708@ebi.ac.uk> yann bizouerne wrote: > I want to work with EMBL and EMBLnew. I have index the EMBL files and > the EMBL new filers in separate directories.(/EMBL/ & /EMBLnew/). > > I did this because I just want to re-index EMBLnew when new sequences > are coming, and not all the sequences (EMBL + EMBLnew) > > Now I want to interogate againts these two databases with one request. > How could I do such thing ? Is it the good way to work with EMBL or not ? This is my next EMBOSS task!!! You can of course already do this with SRS. If you put both databases together, EMBOSS will have problems with duplicate IDs. For now, the EMBOSS solution is to use "whichdb" which will search all your databases for an entry. If it reports an entry in EMBL and EMBLNEW you can use the EMBLNEW entry. I am planning to extend the EMBOSS "USA" syntax to include features of the SRS query language, including a query of more than one database, more than one field, and more than one text string (and of course ... more than one query) To query EMBL and EMBLNEW you also need to exclude matching entries - I can add that by excluding matching IDs from EMBL. I hope to do this by defining an "EMBLALL" database to make life easier for users. SWISSPROT/SWISSNEW/SPTREMBL is more difficult because the matches have to be by accession number. There is already a non-redundant "swall" database available so this is not such a high priority and may have to wait for a way to link databases in EMBOSS (but the internal EMBOSS code does allow for this kind of extension). Hope this helps, Peter Rice From gvasudevan at medarex.com Mon Mar 17 21:50:04 2003 From: gvasudevan at medarex.com (Vasudevan, Geetha) Date: Mon, 17 Mar 2003 13:50:04 -0800 Subject: hydropathicity... Message-ID: <8249C3256E593D4FB066BB9998D9F7E41CF157@ca2-fs03.ca2.2k.medarex.com> I am trying to calulate normalized consensus hydropathicity values for a given seq using PEPINFO. It uses Eaa_hyropathy.dat file which has Kyte-Doo indices, OHM and consensus values. Are the consensus ones same as normalized consensus scale (ref:Eisenberg D.; Schwarz E.; Komarony M.; Wall R. J. Mol. Biol. 1984, 179, 125-142) ? Thanks for any feedback. -Geetha. From Wiepert.Mathieu at mayo.edu Mon Mar 17 21:57:37 2003 From: Wiepert.Mathieu at mayo.edu (Wiepert, Mathieu) Date: Mon, 17 Mar 2003 15:57:37 -0600 Subject: specifying octanol output filename Message-ID: <2F41CC6C9777D311ACBD009027B108EA0541C59B@excsrv32.mayo.edu> Hi, Is there a way to redirect octanol output to a filename of my choosing? I looked through the Command line docs but couldn't find anything. I thought there was a global option like -output or -outfile, but I can't seem to get anything to work with octanol. All output is named octanol.1.png (used -graph png option). Simple enough to add a second line of code to rename the file, but seems different than the other programs I have used so far. While I am at it, I have one file with many sequences, in fasta format. Can octanol create output for all the sequences with one call? I can easily get around this as well, but many programs seem to take files with many sequences, thought I would ask. Thanks, -Mat From stefanielager at fastmail.ca Tue Mar 18 06:14:03 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Tue, 18 Mar 2003 01:14:03 -0500 (EST) Subject: specifying octanol output filename Message-ID: <3E76B92B.00015B.93248@ns.interchange.ca> Try octanol -help -verbose then you see that you get some "-graph related qualifiers", and you can use -goutfile2 to specify an output file. Stefanie > Hi, > > Is there a way to redirect octanol output to a filename of my > choosing? I looked through the Command line docs but couldn't > find anything. I thought there was a global option like -output > or -outfile, but I can't seem to get anything to work with > octanol. All output is named octanol.1.png (used -graph png > option). Simple enough to add a second line of code to rename the > file, but seems different than the other programs I have used so > far. > > While I am at it, I have one file with many sequences, in fasta > format. Can octanol create output for all the sequences with one > call? I can easily get around this as well, but many programs > seem to take files with many sequences, thought I would ask. > > Thanks, _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From stefanielager at fastmail.ca Tue Mar 18 06:12:05 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Tue, 18 Mar 2003 01:12:05 -0500 (EST) Subject: EMBL and Ensembl Message-ID: <3E76B8B5.00017F.99699@ns.interchange.ca> Hi, I have some problems with the EMBL format output from Ensembl. If I retrieve a LARGE piece of DNA from Ensembl in EMBL format, the SQ line gets so long so it's divided into two SQ lines, this is NOT handled correctly by EMBOSS programs! Some EMBOSS programs gives a warning about illegal characters, others just incorporates the second SQ line in the sequence. It's easy to fix the problem by manual editing, but it would be nice to know it this IS standard EMBL format or if it's Ensembl that's made a mistake? ID 1.77242832-92443803 ENSEMBL; DNA; PLN; 15200972 BP. XX ..... ..... ..... FT misc_feature 14757170..15200972 FT /note="contig 1.92000001-93000000 1..443803(1)" XX SQ Sequence 15200972 BP; 4106479 A; 3111667 C; 3123445 G; 4136833 T; 722548 SQ other; TAGAACTTGC AAATGAGAAA ACAGAGTTCT GTCAAGCTGT GTTAGTGTTT GCCCAACACA 60 _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From Jack.Leunissen at wur.nl Tue Mar 18 10:14:31 2003 From: Jack.Leunissen at wur.nl (Jack Leunissen) Date: Tue, 18 Mar 2003 11:14:31 +0100 Subject: EMBL and Ensembl References: <3E76B8B5.00017F.99699@ns.interchange.ca> Message-ID: <001201c2ed37$2b530340$6b82e089@leunissen> This is definitely NOT correct. There can be only 1 (one) SQ line per entry (see the EMBL user manual ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt). So it is Ensembl that is introducing the mistake; the EMBOSS are right in expecting only one SQ in the entry. Cheers, Jack ----- Original Message ----- From: "Stefanie Lager" To: Sent: Tuesday, March 18, 2003 7:12 AM Subject: EMBL and Ensembl > Hi, > > I have some problems with the EMBL format output from Ensembl. If I > retrieve a LARGE piece of DNA from Ensembl in EMBL format, the SQ line > gets so long so it's divided into two SQ lines, this is NOT handled > correctly by EMBOSS programs! Some EMBOSS programs gives a warning > about illegal characters, others just incorporates the second SQ line > in the sequence. It's easy to fix the problem by manual editing, but > it would be nice to know it this IS standard EMBL format or if it's > Ensembl that's made a mistake? > > ID 1.77242832-92443803 ENSEMBL; DNA; PLN; 15200972 BP. > XX > ..... > ..... > ..... > FT misc_feature 14757170..15200972 > FT /note="contig 1.92000001-93000000 1..443803(1)" > XX > SQ Sequence 15200972 BP; 4106479 A; 3111667 C; 3123445 G; 4136833 T; > 722548 > SQ other; > TAGAACTTGC AAATGAGAAA ACAGAGTTCT GTCAAGCTGT GTTAGTGTTT GCCCAACACA > 60 > > > _________________________________________________________________ > http://fastmail.ca/ - Fast Secure Web Email for Canadians From ame at esbs.u-strasbg.fr Tue Mar 18 10:52:07 2003 From: ame at esbs.u-strasbg.fr (Jean-Christophe AME) Date: Tue, 18 Mar 2003 11:52:07 +0100 Subject: problem with Apple X11beta3 and emboss Message-ID: Hi All, This morning I updated Apple X11 for MAcOSX to beta3 and now when I use an EMBOSS program does require X11 I get the following error: Error in XCreatePixmap: BadDrawable (invalid Pixmap or Window parameter). I recompiled the whole EMBOSS suite with the new AppleX11beta3 SDK but I get the same error. Can someone explain... Is it a problem with Apple X11. It used to work fine before. All the other X11 applications seem to work fine with the beta3. Thanks Jean-Christophe ________________________ Jean-Christophe Am?, PhD U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et Structurale ?cole Sup?rieure de Biotechnologie de Strasbourg P?le API Boulevard S?bastien-Brant 67400 Illkirch France tel.: 33 3 90 24 47 05 Fax.: 33 3 90 24 46 86 http://parplink.u-strasbg.fr http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1008 bytes Desc: not available URL: From bemis at io.iol.unh.edu Tue Mar 18 15:06:05 2003 From: bemis at io.iol.unh.edu (Matthew H. Bemis) Date: Tue, 18 Mar 2003 10:06:05 -0500 (EST) Subject: cDNA Vector trim. Message-ID: Hello, I have never used emboss before, and I would like to know if there exists a trimming program to cut a vector off some sequence samples I have, and stop trimming at my LokI site. I've compiled the full set of tools on a new Mac OSX, and I have all of them available to me. any advice would be greatly appreciated thanks, matt bemis From d.m.a.martin at dundee.ac.uk Tue Mar 18 15:26:36 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Tue, 18 Mar 2003 15:26:36 +0000 Subject: cDNA Vector trim. In-Reply-To: Message-ID: On 18/3/03 3:06 pm, "Matthew H. Bemis" wrote: > Hello, > I have never used emboss before, and I would like to know if there exists > a trimming program to cut a vector off some sequence samples I have, and > stop trimming at my LokI site. I've compiled the full set of tools on a > new Mac OSX, and I have all of them available to me. > any advice would be greatly appreciated $ wossname vector Finds programs by keywords in their one-line documentation SEARCH FOR 'VECTOR' vectorstrip Strips out DNA between a pair of vector sequences regards ..d > thanks, > matt bemis > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From alfons at elmeuportal.net Tue Mar 18 16:36:08 2003 From: alfons at elmeuportal.net (alfons at elmeuportal.net) Date: Tue, 18 Mar 2003 09:36:08 -0700 (MST) Subject: Help! Message-ID: <1224.158.109.54.199.1048005368.squirrel@www.elmeuportal.net> Hi! I would want to know if exist a program, in emboss, that make groups of genes functions in the cromosome of Drosophyla. Thanks, Alfons. From gvasudevan at medarex.com Wed Mar 19 17:39:03 2003 From: gvasudevan at medarex.com (Vasudevan, Geetha) Date: Wed, 19 Mar 2003 09:39:03 -0800 Subject: multiple seqs in fasta fmt... Message-ID: <8249C3256E593D4FB066BB9998D9F7E41CF165@ca2-fs03.ca2.2k.medarex.com> Is it possible to read multiple seqs in fasta fmt to the emboss program "pepinfo" to produce a -goutfile for hydropathy values ? thanks in advance. -geetha. From pmr at ebi.ac.uk Wed Mar 19 17:43:38 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 19 Mar 2003 17:43:38 +0000 Subject: multiple seqs in fasta fmt... References: <8249C3256E593D4FB066BB9998D9F7E41CF165@ca2-fs03.ca2.2k.medarex.com> Message-ID: <3E78AC4A.8060602@ebi.ac.uk> Vasudevan, Geetha wrote: > Is it possible to read multiple seqs in fasta fmt to the emboss program "pepinfo" > to produce a -goutfile for hydropathy values ? No ... because pepinfo creates two graphs and making that work for multiple sequence input is very tricky. This is why pepinfo only reads a single sequence (but you can put ":id" after the filename to say which FASTA file entry you want, of use dbifasta to index the file as a database) But ... it is (relatively) easy to modify pepwindow to generate hydropathy plots or data for multiple sequences. How many sequences do you have in mind? regards, Peter From Wiepert.Mathieu at mayo.edu Wed Mar 19 17:47:50 2003 From: Wiepert.Mathieu at mayo.edu (Wiepert, Mathieu) Date: Wed, 19 Mar 2003 11:47:50 -0600 Subject: multiple seqs in fasta fmt... Message-ID: <2F41CC6C9777D311ACBD009027B108EA0541C5CB@excsrv32.mayo.edu> Hi, This may be simplistic, but I had the same problem with octanol, many fasta formatted sequence in one file. so I used seqretsplit on the file, and then did this at a command line for i in *.fasta;do octanol -sequence $i -graph png ?auto -goutfile2 $i.png;done Not pretty, but it worked. -mat -----Original Message----- From: Peter Rice [mailto:pmr at ebi.ac.uk] Sent: Wednesday, March 19, 2003 11:44 AM To: Vasudevan, Geetha Cc: emboss at hgmp.mrc.ac.uk Subject: Re: multiple seqs in fasta fmt... Vasudevan, Geetha wrote: > Is it possible to read multiple seqs in fasta fmt to the emboss program "pepinfo" > to produce a -goutfile for hydropathy values ? No ... because pepinfo creates two graphs and making that work for multiple sequence input is very tricky. This is why pepinfo only reads a single sequence (but you can put ":id" after the filename to say which FASTA file entry you want, of use dbifasta to index the file as a database) But ... it is (relatively) easy to modify pepwindow to generate hydropathy plots or data for multiple sequences. How many sequences do you have in mind? regards, Peter From pmr at ebi.ac.uk Wed Mar 19 17:50:20 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 19 Mar 2003 17:50:20 +0000 Subject: multiple seqs in fasta fmt... References: <2F41CC6C9777D311ACBD009027B108EA0541C5CB@excsrv32.mayo.edu> Message-ID: <3E78ADDC.9080606@ebi.ac.uk> Wiepert, Mathieu wrote: > Hi, > > This may be simplistic, but I had the same problem with octanol, many fasta formatted sequence in one file. so I used seqretsplit on the file, and then did this at a command line > > for i in *.fasta;do octanol -sequence $i -graph png ?auto -goutfile2 $i.png;done I suspect the question is how to get all the plots into one postscript file - which means reading the full FASTA file in one run ... but this would be a good approach too. Peter From gvasudevan at medarex.com Wed Mar 19 18:16:40 2003 From: gvasudevan at medarex.com (Vasudevan, Geetha) Date: Wed, 19 Mar 2003 10:16:40 -0800 Subject: multiple seqs in fasta fmt... Message-ID: <8249C3256E593D4FB066BB9998D9F7E41CF166@ca2-fs03.ca2.2k.medarex.com> I would like to use pepinfo rather than pepwindow because, pepwindow uses Enakai.dat (Kyte-DooLittle) and I want to use Eaa_hydropathy.dat(consensus Eisenberg) used by pepinfo. pepwindow -datafile Eaa_hydropathy.dat ( raises exception-- Uncaught exception: Assertion failed, raised at ajmem.c:93) And I have 100s of seqs to calculate this. -GV -----Original Message----- From: Peter Rice [mailto:pmr at ebi.ac.uk] Sent: Wed 3/19/2003 9:43 AM To: Vasudevan, Geetha Cc: emboss at hgmp.mrc.ac.uk Subject: Re: multiple seqs in fasta fmt... Vasudevan, Geetha wrote: > Is it possible to read multiple seqs in fasta fmt to the emboss program "pepinfo" to produce a -goutfile for hydropathy values ? No ... because pepinfo creates two graphs and making that work for multiple sequence input is very tricky. This is why pepinfo only reads a single sequence (but you can put ":id" after the filename to say which FASTA file entry you want, of use dbifasta to index the file as a database) But ... it is (relatively) easy to modify pepwindow to generate hydropathy plots or data for multiple sequences. How many sequences do you have in mind? regards, Peter From gvasudevan at medarex.com Wed Mar 19 19:12:26 2003 From: gvasudevan at medarex.com (Vasudevan, Geetha) Date: Wed, 19 Mar 2003 11:12:26 -0800 Subject: index fasta DB file.. Message-ID: <8249C3256E593D4FB066BB9998D9F7E41CF168@ca2-fs03.ca2.2k.medarex.com> Is is possible to index using dbifasta, a fasta DB file whose header is like this, (>DBID 00001, species followed by description) ? And, is it possible to "retrieve" a sequence from this file, given a "DBID number"? thanks for all your suggestions. -Geetha. From kellert at ohsu.edu Wed Mar 19 23:12:45 2003 From: kellert at ohsu.edu (Thomas Keller) Date: Wed, 19 Mar 2003 15:12:45 -0800 Subject: microarray primer design Message-ID: <4B68B919-5A60-11D7-8736-0003930405E2@ohsu.edu> I've always designed primers one at a time. Usually with the very excellent program Oligo (W. Rychlik). I've got eprimer3/primer3 working but I'm not sure how to use it to find hybridization oligos for use with microarrays. I'd be grateful for suggestions, since I've got about 1,300 oligos to design. Thanks, Tom K. From grimplet at ensam.inra.fr Thu Mar 20 08:10:56 2003 From: grimplet at ensam.inra.fr (=?iso-8859-1?q?j=E9r=F4me=20Grimplet?=) Date: Thu, 20 Mar 2003 09:10:56 +0100 Subject: microarray primer design In-Reply-To: <4B68B919-5A60-11D7-8736-0003930405E2@ohsu.edu> References: <4B68B919-5A60-11D7-8736-0003930405E2@ohsu.edu> Message-ID: <200303200910.56160.grimplet@ensam.inra.fr> Le Jeudi 20 Mars 2003 00:12, Thomas Keller a ?crit : > I've always designed primers one at a time. Usually with the very > excellent program Oligo (W. Rychlik). > I've got eprimer3/primer3 working but I'm not sure how to use it to > find hybridization oligos for use with microarrays. > I'd be grateful for suggestions, since I've got about 1,300 oligos to > design. > Thanks, > Tom K. Hi, Try OligoArray...... http://berry.engin.umich.edu/oligoarray/ -- J?r?me Grimplet Laboratoire de Biochimie M?tabolique et Technologie UMR Sciences Pour l'Oenologie 2, Place Viala 34060 Montpellier Cedex 01 Tel: 33(0)4.99.61.27.56 Fax: 33(0)4.99.61.28.57 grimplet at ensam.inra.fr From gwilliam at hgmp.mrc.ac.uk Thu Mar 20 09:28:20 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 20 Mar 2003 09:28:20 +0000 Subject: microarray primer design References: <4B68B919-5A60-11D7-8736-0003930405E2@ohsu.edu> Message-ID: <3E7989B4.EA92BA49@hgmp.mrc.ac.uk> Microarrays typically use oligos of about 50 to 60 bp in length. The maximum length of an oligo that can be found by the primer3 program is 35. This limit is governed by the maximum oligo size for which primer3's melting-temperature is valid. Gary Thomas Keller wrote: > > I've always designed primers one at a time. Usually with the very > excellent program Oligo (W. Rychlik). > I've got eprimer3/primer3 working but I'm not sure how to use it to > find hybridization oligos for use with microarrays. > I'd be grateful for suggestions, since I've got about 1,300 oligos to > design. > Thanks, > Tom K. -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From pmr at ebi.ac.uk Thu Mar 20 11:44:43 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Mar 2003 11:44:43 +0000 Subject: multiple seqs in fasta fmt... References: <8249C3256E593D4FB066BB9998D9F7E41CF166@ca2-fs03.ca2.2k.medarex.com> Message-ID: <3E79A9AB.8080408@ebi.ac.uk> Vasudevan, Geetha wrote: > I would like to use pepinfo rather than pepwindow because, > pepwindow uses Enakai.dat (Kyte-DooLittle) and I want to use > Eaa_hydropathy.dat(consensus Eisenberg) used by pepinfo. > pepwindow -datafile Eaa_hydropathy.dat ( raises exception-- > Uncaught exception: Assertion failed, raised at ajmem.c:93) > > And I have 100s of seqs to calculate this. Ah ... but pepwindow can use any of the "Nakai et al." database of amino acid parameters - these used to be in a database called "NAKAI" but are now in one called "AAINDEX". EMBOSS has a program "aaindexextract" that takes data from this database and makes it available for pepwindow. It appears this enhancement did not make it into the pepwindow documentation... it will do today!!! 1. FTP the AAINDEX database from Japan: ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1 2. Run aaindexextract with the aaindex1 file as input (or ask whoever installs EMBOSS to run it) 3. Run pepwindow with -datafile swer830101 and (to match pepinfo) -hwindow 9 (or whatever value you use for -length in pepinfo) This is the middle plot pepinfo produces. ... and of course we should look into why pepinfo and pepwindow use different window lengths, and different option names. Hope this helps. Peter Rice From bemis at io.iol.unh.edu Thu Mar 20 14:47:51 2003 From: bemis at io.iol.unh.edu (Matthew H. Bemis) Date: Thu, 20 Mar 2003 09:47:51 -0500 (EST) Subject: cDNA Vector trim. In-Reply-To: References: Message-ID: Hi, Thanks for the advice! The programs work great. Now I have all this data and I have phred( phd.1 ) files that I'd like to align and look for mismatches( high score mismatches ). Is there software for this? I have four file types to work with here: .seq fasta phd.1 scf if there software out there for looking for high quality mutations? writing software is not out of the question for me either. I am a cs graduate student, but I'd rather not re-invent the wheel. thanks in advance! Matt Bemis On Tue, 18 Mar 2003, David Martin wrote: > On 18/3/03 3:06 pm, "Matthew H. Bemis" wrote: > > > Hello, > > I have never used emboss before, and I would like to know if there exists > > a trimming program to cut a vector off some sequence samples I have, and > > stop trimming at my LokI site. I've compiled the full set of tools on a > > new Mac OSX, and I have all of them available to me. > > any advice would be greatly appreciated > > $ wossname vector > Finds programs by keywords in their one-line documentation > SEARCH FOR 'VECTOR' > vectorstrip Strips out DNA between a pair of vector sequences > > > regards > > ..d > > > thanks, > > matt bemis > > > > -- > David Martin PhD > Bioinformatics Scientific Officer > Post-Genomics and Molecular Interactions Centre > University of Dundee > From mad at biol.unlp.edu.ar Thu Mar 20 15:06:11 2003 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Thu, 20 Mar 2003 12:06:11 -0300 Subject: =?ISO-8859-1?Q?=BFEMBOSS_first_release=3F?= Message-ID: <3E79D8E3.4090107@biol.unlp.edu.ar> Hi, I'm preparing a presentation on EMBOSS and I would like to know when was the first release of it. In http://www.emboss.org in the "History" page isn't mentioned, only that it evolved from EGCG. Thanks. Regards, martin -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From lmullan at hgmp.mrc.ac.uk Thu Mar 20 15:05:04 2003 From: lmullan at hgmp.mrc.ac.uk (Lisa Mullan) Date: Thu, 20 Mar 2003 15:05:04 +0000 (GMT) Subject: =?ISO-8859-1?Q?=BFEMBOSS_first_release=3F?= In-Reply-To: <3E79D8E3.4090107@biol.unlp.edu.ar> Message-ID: As far as I know it was St. Swithans Day (15th July) 2000 - that's what I tell people on the courses, so unless Alan was drunk when he told me................!! Lisa PS: If you need any material, let me know. Lisa Mullan HGMP Resource Centre Hinxton, Cambridge, CB10 1SB Tel: 01223 494526 Email: lmullan at hgmp.mrc.ac.uk On Thu, 20 Mar 2003, [ISO-8859-1] Mart?n Sarachu wrote: > Hi, > > I'm preparing a presentation on EMBOSS and I would like to know when was > the first release of it. In http://www.emboss.org in the "History" page > isn't mentioned, only that it evolved from EGCG. > > Thanks. > > > Regards, > > martin > > -- > Mart?n Sarachu > mad at biol.unlp.edu.ar > EMBNet Argentina > http://www.ar.embnet.org > From pmr at ebi.ac.uk Thu Mar 20 15:06:03 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Mar 2003 15:06:03 +0000 Subject: =?ISO-8859-1?Q?=BFEMBOSS_first_release=3F?= References: <3E79D8E3.4090107@biol.unlp.edu.ar> Message-ID: <3E79D8DB.7010504@ebi.ac.uk> Mart?n Sarachu wrote: > I'm preparing a presentation on EMBOSS and I would like to know when was > the first release of it. In http://www.emboss.org in the "History" page > isn't mentioned, only that it evolved from EGCG. I remember it well. EMBOSS 1.0.0 was July 15th 2000. Saint Swithin's Day ... and the day I handed over the project to Alan when I left the Sanger Centre. Of course, the beta versions were around for a couple of years before that. I demonstrated 0.0.c (if memory serves) in August 1998. Alan ... do you have a copy of the announcement? Maybe it could go on the website :-) regards, Peter From d.m.a.martin at dundee.ac.uk Thu Mar 20 15:10:48 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 20 Mar 2003 15:10:48 +0000 Subject: cDNA Vector trim. In-Reply-To: Message-ID: On 20/3/03 2:47 pm, "Matthew H. Bemis" wrote: > Hi, > Thanks for the advice! The programs work great. Now I have all this data > and I have phred( phd.1 ) files that I'd like to align and look for > mismatches( high score mismatches ). Is there software for this? > I have four file types to work with here: > .seq > fasta > phd.1 > scf > if there software out there for looking for high quality mutations? > writing software is not out of the question for me either. I am a cs > graduate student, but I'd rather not re-invent the wheel. > thanks in advance! Checkout the staden package which does all sorts of things you would find useful, in particular pregap4 and gap4. ..d > Matt Bemis > > On Tue, 18 Mar 2003, David Martin wrote: > >> On 18/3/03 3:06 pm, "Matthew H. Bemis" wrote: >> >>> Hello, >>> I have never used emboss before, and I would like to know if there exists >>> a trimming program to cut a vector off some sequence samples I have, and >>> stop trimming at my LokI site. I've compiled the full set of tools on a >>> new Mac OSX, and I have all of them available to me. >>> any advice would be greatly appreciated >> >> $ wossname vector >> Finds programs by keywords in their one-line documentation >> SEARCH FOR 'VECTOR' >> vectorstrip Strips out DNA between a pair of vector sequences >> >> >> regards >> >> ..d >> >>> thanks, >>> matt bemis >>> >> >> -- >> David Martin PhD >> Bioinformatics Scientific Officer >> Post-Genomics and Molecular Interactions Centre >> University of Dundee >> > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From d.m.a.martin at dundee.ac.uk Thu Mar 20 15:14:40 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 20 Mar 2003 15:14:40 +0000 Subject: =?ISO-8859-1?B?vw==?=EMBOSS first release? In-Reply-To: Message-ID: On 20/3/03 3:05 pm, "Lisa Mullan" wrote: > As far as I know it was St. Swithans Day (15th July) 2000 - that's what I > tell people on the courses, so unless Alan was drunk when he told > me................!! > Well I would have been as that was my birthday.. That was release 1.0.0 AFAIR. 0.0.4 was floating around for at least a year before that (and earlier incarnations before that). The first useable production release is a more subjective question.. probably about christmas 1999. The changes were flying thick and fast back then.. 2 or three updates a week. ..d > Lisa > > > PS: If you need any material, let me know. > > Lisa Mullan > HGMP Resource Centre > Hinxton, > Cambridge, CB10 1SB > Tel: 01223 494526 > Email: lmullan at hgmp.mrc.ac.uk > > On Thu, 20 Mar 2003, [ISO-8859-1] Mart?n Sarachu wrote: > >> Hi, >> >> I'm preparing a presentation on EMBOSS and I would like to know when was >> the first release of it. In http://www.emboss.org in the "History" page >> isn't mentioned, only that it evolved from EGCG. >> >> Thanks. >> >> >> Regards, >> >> martin >> >> -- >> Mart?n Sarachu >> mad at biol.unlp.edu.ar >> EMBNet Argentina >> http://www.ar.embnet.org >> > > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From ableasby at hgmp.mrc.ac.uk Thu Mar 20 15:15:55 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 20 Mar 2003 15:15:55 GMT Subject: =?ISO-8859-1?Q?=BFEMBOSS_first_release=3F?= Message-ID: <200303201515.h2KFFtF21824@bromine.hgmp.mrc.ac.uk> I'll see if I can find an announcement but I'm not hopeful. As for being drunk, Lisa knows perfectly well that I don't drink alcohol (others may not). Cheers Alan From gwilliam at hgmp.mrc.ac.uk Thu Mar 20 15:19:16 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 20 Mar 2003 15:19:16 +0000 Subject: =?iso-8859-1?Q?=BFEMBOSS?= first release? References: <200303201515.h2KFFtF21824@bromine.hgmp.mrc.ac.uk> Message-ID: <3E79DBF4.204850BC@hgmp.mrc.ac.uk> Announcement attached. Gary ableasby at hgmp.mrc.ac.uk wrote: > > I'll see if I can find an announcement but I'm not hopeful. > > As for being drunk, Lisa knows perfectly well that I don't > drink alcohol (others may not). > > Cheers > Alan -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From pmiguel at purdue.edu Thu Mar 20 15:16:47 2003 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Thu, 20 Mar 2003 10:16:47 -0500 Subject: cDNA Vector trim. References: Message-ID: <3E79DB5F.3090400@purdue.edu> David Martin wrote: >On 20/3/03 2:47 pm, "Matthew H. Bemis" wrote: > > > >>Hi, >>Thanks for the advice! The programs work great. Now I have all this data >>and I have phred( phd.1 ) files that I'd like to align and look for >>mismatches( high score mismatches ). Is there software for this? >>I have four file types to work with here: >>.seq >>fasta >>phd.1 >>scf >>if there software out there for looking for high quality mutations? >>writing software is not out of the question for me either. I am a cs >>graduate student, but I'd rather not re-invent the wheel. >>thanks in advance! >> >> > >Checkout the staden package which does all sorts of things you would find >useful, in particular pregap4 and gap4. > >..d > [...] If you have the phredPhrap package already, you might find cross_match sufficient. Convert your phd files to a fasta and qual files using phd2fasta. When you do the comparsion with cross_match, a large table of the quality values of the mis-matches is generated. Not sure if it is what you are looking for. I generally am looking for ways to filter out this output. Help is at www.phrap.org. Phillip SanMiguel Purdue Genomics Core From d.m.a.martin at dundee.ac.uk Thu Mar 20 15:22:28 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 20 Mar 2003 15:22:28 +0000 Subject: FW: EMBOSS has moved to HGMP In-Reply-To: <200007152229.XAA19252@bromine.hgmp.mrc.ac.uk> Message-ID: Here is the move from Sanger to HGMP and a hint of a 1.0 release -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee ------ Forwarded Message From: Date: Sat, 15 Jul 2000 23:29:33 +0100 (BST) To: emboss at hgmp.mrc.ac.uk Subject: EMBOSS has moved to HGMP Dear EMBOSS folk, Yes, EMBOSS has indeed moved. Please note the new address for the web pages. It is: http://www.uk.embnet.org/Software/EMBOSS or if you prefer http://www.hgmp.mrc.ac.uk/Software/EMBOSS they are the same address. Similarly the ftp server becomes: ftp://ftp.uk.embnet.org/pub/EMBOSS or ftp://ftp.hgmp.mrc.ac.uk/pub/EMBOSS Why the move? It is because Peter Rice and Ian Longden have both just gone into the commercial sector. Peter has gone to Lion and Ian to Informatica. This left noone at Sanger with the experience to maintain EMBOSS therefore it finds a welcome home with the HGMP developers. I surely speak for all of us when I thank Peter and Ian for their work... although Peter will still be active with EMBOSS from the Lion point of view so this is neither an obituary or E.J. Thribb poem. Both still have their Sanger usernames intact for now. And so on to the changes. You will notice a different look and feel to the web pages. This is in preparation for the imminent announcement of Release 1.0.0. You will see this reflected in the filename of EMBOSS on the ftp server. It is EMBOSS-1.0.0.tar.gz N.B: As of this distribution there is an extra 'emboss' directory level at the top. This is to allow the --prefix configuration option to (optionally) install directories there. The instructions for use of the CVS server have also changed. Please read the new instructions on the web pages if you use this method. This server also has the extra directory mentioned above. Also note that there is no alias for cvs.hgmp.mrc.ac.uk at the moment i.e. cvs.uk.embnet.org will not work but the former will. The mail list addresses have changed accordingly. They are: emboss at uk.embnet.org emboss-dev at uk.embnet.org or emboss at hgmp.mrc.ac.uk emboss-dev at hgmp.mrc.ac.uk All the subscription addresses have been moved over. The majordomo server at our site works in the same way as on the Sanger site. N.B.: Until the Sanger site change their links to redirect to HGMP their site is still active. It is not being updated though. To get the latest updates you must use the new addresses. I am bound to have forgotten something as we've all had to work like demons to move things over and get to a stage where we can advertise release 1.0.0. I will post if anything important springs to mind. Finally, it is St Swithins Day so, if the new service works today it will probably work for the next 40. If not you can always email: emboss-bug at uk.embnet.org or emboss-bug at hgmp.mrc.ac.uk Cheers Alan HGMP ------ End of Forwarded Message From lmullan at hgmp.mrc.ac.uk Thu Mar 20 15:24:48 2003 From: lmullan at hgmp.mrc.ac.uk (Lisa Mullan) Date: Thu, 20 Mar 2003 15:24:48 +0000 (GMT) Subject: =?ISO-8859-1?Q?=BFEMBOSS_first_release=3F?= In-Reply-To: <200303201515.h2KFFtF21824@bromine.hgmp.mrc.ac.uk> Message-ID: Exactly - so everyone knows that what you told me must be true!!! Lisa Lisa Mullan HGMP Resource Centre Hinxton, Cambridge, CB10 1SB Tel: 01223 494526 Email: lmullan at hgmp.mrc.ac.uk On Thu, 20 Mar 2003 ableasby at hgmp.mrc.ac.uk wrote: > I'll see if I can find an announcement but I'm not hopeful. > > As for being drunk, Lisa knows perfectly well that I don't > drink alcohol (others may not). > > Cheers > Alan > From pmr at ebi.ac.uk Thu Mar 20 16:15:04 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Mar 2003 16:15:04 +0000 Subject: index fasta DB file.. References: <8249C3256E593D4FB066BB9998D9F7E41CF168@ca2-fs03.ca2.2k.medarex.com> Message-ID: <3E79E908.4080305@ebi.ac.uk> Vasudevan, Geetha wrote: > Is is possible to index using dbifasta, a fasta DB file whose header is like this, > > (>DBID 00001, species followed by description) ? > > And, is it possible to "retrieve" a sequence from this file, given a "DBID number"? The syntax must match something dbifasta understands. See the dbifasta documentation for more information. DBID should be some 'standard' fasta identifier. EMBOSS is happy with anything in test/data/testids.fasta or test/data/testids.ncbi For example: >dbname:id or >id In both cases, filename:id will extract that ID You can also read the accession number, if it appears as the next text on the line: >DBID A00001 species followed by description then you can use filename:a00001 ... but this only works if (a) the accession number is a valid EMBL/SwissProt accession number and (b) it has white space either side. This format of fasta file is (or was) used by ACEDB at the Sanger Centre. Hope this helps, Peter Rice From gwilliam at hgmp.mrc.ac.uk Thu Mar 20 16:50:48 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 20 Mar 2003 16:50:48 +0000 Subject: =?iso-8859-1?Q?=BFEMBOSS?= first release? References: <3E79D8E3.4090107@biol.unlp.edu.ar> Message-ID: <3E79F168.8F10DAD8@hgmp.mrc.ac.uk> Some of the early milestones for EMBOSS are now documented briefly in: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/history.html Gary Mart?n Sarachu wrote: > > Hi, > > I'm preparing a presentation on EMBOSS and I would like to know when was > the first release of it. In http://www.emboss.org in the "History" page > isn't mentioned, only that it evolved from EGCG. > > Thanks. > > Regards, > > martin > > -- > Mart?n Sarachu > mad at biol.unlp.edu.ar > EMBNet Argentina > http://www.ar.embnet.org -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From aengus.stewart at cancer.org.uk Thu Mar 20 17:27:31 2003 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Thu, 20 Mar 2003 17:27:31 +0000 Subject: DataLib management Message-ID: <3E79FA03.F529F703@cancer.org.uk> Hi, Sorry in advance folks, but I am making a concerted effort to set up the datalibs for access by EMBOSS and as a result it has prompted a few questions. First of all a comment - I have had a look at the documentation for both dbiflat and dbigcg, and neither makes any note of the fact that both ACNUM and ID fields are indexed by default. In fact ID is not really mentioned at all so when you look at the documentation for the '-fields' flag it appears that there are only 5 possible fields to index. A small point, there is an inconsistency between the allowed values for -fields and the values for the fields: tag in emboss.default -fields flag can use any of - acnum,seqvn,des,keyword,taxon fields: tag can use any of - acc id sv des org key I know they dont have to be the same, it just seemed odd. showdb -fields returns Died: unknown qualifier -fields Also dbigcg/dbiflat asks for the release number and date. I would like showdb to pick this information up but the only way I can see of doing this is a search/replace on 'release:X.Y' in emboss.default What does dbigcg/dbiflat do with the release/date info? Sorry again for all the queries. Aengus -- -------------------------------------------------------------------------- Aengus Stewart aengus.stewart at DELcancerETE.org.uk Computational Genome Analysis Laboratory Tel: +44 (0)20 7269 3679 Cancer Research UK Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK -------------------------------------------------------------------------- From pmr at ebi.ac.uk Thu Mar 20 17:35:03 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 20 Mar 2003 17:35:03 +0000 Subject: DataLib management References: <3E79FA03.F529F703@cancer.org.uk> Message-ID: <3E79FBC7.7050508@ebi.ac.uk> Aengus Stewart wrote: > First of all a comment - I have had a look at the documentation for both > dbiflat and dbigcg, and neither makes any note of the fact that both > ACNUM and ID fields are indexed by default. Will be fixed. Thanks. > A small point, there is an inconsistency between the allowed values for > -fields and the values for the fields: tag in emboss.default > > I know they dont have to be the same, it just seemed odd. Should be consistent. One is the names for the query syntax (same as in SRS) the other is the name used in the EMBLCD format index files. I would prefer to use the query language names (id acc sv des org key) which means just changing the prompts for dbiflat and friends. Any other votes? > showdb -fields > returns > Died: unknown qualifier -fields This works in the current developers release, which is what the EMBOSS web pages always refer to. > What does dbigcg/dbiflat do with the release/date info? It is part of the EMBLCD (and Staden) index file header. EMBOSS does not use it at present - but I would like to start making use of it. It is not yet clear whether there should be a release number in the DBNAME definition in emboss.defaults - it is convenient to save asking the EMBLCD index (or SRS or whatever) but would need to be maintained. Let's just say "I'm working on a solution" :-) Hope this helps, Peter From aengus.stewart at cancer.org.uk Fri Mar 21 14:39:55 2003 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Fri, 21 Mar 2003 14:39:55 +0000 Subject: Non-sequence DataLibs References: <3E79FA03.F529F703@cancer.org.uk> Message-ID: <3E7B243B.9A97188A@cancer.org.uk> Hi, I was wondering whether EMBOSS has plans to handle biological structured record data like GO, UNIGENE etc. I was playing around with setting up DBs with methodquery:srswww format: text url:"http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz" but of course retrieving things with seqret doesnt work and entret just produces an empty file. Regards Aengus From ableasby at hgmp.mrc.ac.uk Fri Mar 21 14:50:48 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 21 Mar 2003 14:50:48 GMT Subject: Non-sequence DataLibs Message-ID: <200303211450.h2LEomw28312@bromine.hgmp.mrc.ac.uk> New fields have recently been added to the emboss.defaults definitions as a preliminary step towards handling non-sequence datalibs. So, the answer is that the intention is there but its in the very early stages of development. Alan From aengus.stewart at cancer.org.uk Fri Mar 21 17:51:35 2003 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Fri, 21 Mar 2003 17:51:35 +0000 Subject: Problem with EMBOSS_ROOT References: <200303211450.h2LEomw28312@bromine.hgmp.mrc.ac.uk> Message-ID: <3E7B5127.DA2F05F8@cancer.org.uk> I know its Friday and its well past 5 O'clock but....... I have instances of EMBOSS on 2 machines with the same OS/setup so I just copied the bin/lib/share and then attempted export EMBOSS_ROOT=/path/to/dir/containing/emboss.default on the non-compilation machine unfortunately showdb wasnt too happy. I did separate compilations to sort it but I thought I should mention the EMBOSS_ROOT problem. Aengus -- -------------------------------------------------------------------------- Aengus Stewart aengus.stewart at DELcancerETE.org.uk Computational Genome Analysis Laboratory Tel: +44 (0)20 7269 3679 Cancer Research UK Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK -------------------------------------------------------------------------- From bemis at io.iol.unh.edu Sat Mar 22 17:25:09 2003 From: bemis at io.iol.unh.edu (Matthew H. Bemis) Date: Sat, 22 Mar 2003 12:25:09 -0500 (EST) Subject: cDNA Vector trim. In-Reply-To: References: Message-ID: David, thanks for the info. I've read up on gap4, and it does look like I'll be using this, but I am encountering XFree86 issues on our macosx server. I am an avid X user, but on linux. Using bash I export the display to the correct name, and i try to add the local host to xauth...well I really have been trying to just xhost + the world. The program gap4 will not start. any ideas?? On Thu, 20 Mar 2003, David Martin wrote: > On 20/3/03 2:47 pm, "Matthew H. Bemis" wrote: > > > Hi, > > Thanks for the advice! The programs work great. Now I have all this data > > and I have phred( phd.1 ) files that I'd like to align and look for > > mismatches( high score mismatches ). Is there software for this? > > I have four file types to work with here: > > .seq > > fasta > > phd.1 > > scf > > if there software out there for looking for high quality mutations? > > writing software is not out of the question for me either. I am a cs > > graduate student, but I'd rather not re-invent the wheel. > > thanks in advance! > > Checkout the staden package which does all sorts of things you would find > useful, in particular pregap4 and gap4. > > ..d > > > Matt Bemis > > > > On Tue, 18 Mar 2003, David Martin wrote: > > > >> On 18/3/03 3:06 pm, "Matthew H. Bemis" wrote: > >> > >>> Hello, > >>> I have never used emboss before, and I would like to know if there exists > >>> a trimming program to cut a vector off some sequence samples I have, and > >>> stop trimming at my LokI site. I've compiled the full set of tools on a > >>> new Mac OSX, and I have all of them available to me. > >>> any advice would be greatly appreciated > >> > >> $ wossname vector > >> Finds programs by keywords in their one-line documentation > >> SEARCH FOR 'VECTOR' > >> vectorstrip Strips out DNA between a pair of vector sequences > >> > >> > >> regards > >> > >> ..d > >> > >>> thanks, > >>> matt bemis > >>> > >> > >> -- > >> David Martin PhD > >> Bioinformatics Scientific Officer > >> Post-Genomics and Molecular Interactions Centre > >> University of Dundee > >> > > > > -- > David Martin PhD > Bioinformatics Scientific Officer > Post-Genomics and Molecular Interactions Centre > University of Dundee > From pmr at ebi.ac.uk Mon Mar 24 10:01:45 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 24 Mar 2003 10:01:45 +0000 Subject: Non-sequence DataLibs References: <3E79FA03.F529F703@cancer.org.uk> <3E7B243B.9A97188A@cancer.org.uk> Message-ID: <3E7ED789.9050704@ebi.ac.uk> Aengus Stewart wrote: > I was wondering whether EMBOSS has plans to handle biological structured > record data like GO, UNIGENE etc. > > I was playing around with setting up DBs with > > methodquery:srswww > format: text > url:"http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz" > > but of course retrieving things with seqret doesnt work and entret just > produces an empty file. Yes!!! As Alan said, there are already placeholders for this stuff. I am working on the internals now. Still have to think up an equivalent name to "entret" (which reads sequences as its input type and returns whole entries). "entire" perhaps?) Also need to give a little thought to how to index such databases - aside from using a remote web server (like your example) or local SRS. Hope this helps, Peter From Wiepert.Mathieu at mayo.edu Tue Mar 25 16:05:35 2003 From: Wiepert.Mathieu at mayo.edu (Wiepert, Mathieu) Date: Tue, 25 Mar 2003 10:05:35 -0600 Subject: dbiflat dies...can I restart where it left off? Message-ID: <2F41CC6C9777D311ACBD009027B108EA0541C609@excsrv32.mayo.edu> Hi, I am trying to index a large set of est genbank files with dbiflat. After a few hours of processing, I got Index a flat file database EMBL : EMBL SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew GB : Genbank, DDBJ REFSEQ : Refseq Entry format [SWISS]: genbank Database directory [.]: Wildcard database filename [*.dat]: *.genbank Database name: test Release number [0.0]: .1 Index date [00/00/00]: 03/25/03 Warning: Duplicate ID skipped: 'BF291273' All hits will point to first ID found EMBOSS An error in embdbi.c at line 1074: Error in embDbiSortWriteFields, expected entry BU664328 not found Is there a way to restart this? I didn't use any of the -warning -error -fatal -die -debug options, maybe I should have, so I could see a log. I thought this might be one way to index genbank itself? I have tried bioperl for this, but it takes MUCH longer (as I might have suspected anyway). Haven't tried anything from the ncbi toolkit. -Mat From hkawai at venus.dti.ne.jp Wed Mar 26 13:31:26 2003 From: hkawai at venus.dti.ne.jp (Hironori Kawai) Date: Wed, 26 Mar 2003 22:31:26 +0900 Subject: Retrieiving DB with a list file Message-ID: <200303261330.h2QDU4ME001133@smtp4.dti.ne.jp> Hello When I retrieve some entries from databases using a list file (e.g. seqret @listfile) which consists of both retrievable USAs and irretrievable ones, I meet a kind of problem. If the top-line is a retrievable USA, I can get all retrievable entries, skipping non-retrievable ones. In contrast, if the top-line is irretrievable, programs stop immediately without retrieving any entries inspite of the existence of retrievable USAs on the following lines. I want to make the programs not to terminate even if the top-line is irretrievable. Thanks Hironori Kawai From janef_23 at hotmail.com Wed Mar 26 15:21:26 2003 From: janef_23 at hotmail.com (Jane Fowler) Date: Wed, 26 Mar 2003 15:21:26 +0000 Subject: question about prophecy and profit Message-ID: An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Wed Mar 26 15:23:06 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 26 Mar 2003 15:23:06 +0000 Subject: Retrieiving DB with a list file References: <200303261330.h2QDU4ME001133@smtp4.dti.ne.jp> Message-ID: <3E81C5DA.3000609@ebi.ac.uk> Hironori Kawai wrote: > Hello > > When I retrieve some entries from databases using a list file > (e.g. seqret @listfile) which consists of both retrievable USAs and > irretrievable ones, I meet a kind of problem. > > I want to make the programs not to terminate even if > the top-line is irretrievable. I noticed this one a few days ago. Already fixed in the CVS developers version, and included in the set of QA tests. So "fixed in the next release". Peter From mad at biol.unlp.edu.ar Wed Mar 26 16:43:45 2003 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Wed, 26 Mar 2003 13:43:45 -0300 Subject: OT: where to download transfac database? Message-ID: <3E81D8C1.8000409@biol.unlp.edu.ar> Hi, anyone knows where to download TRANSFAC version 6 public? In the EBI mirror the latest version is TRANSFAC 3.2 Regards, martin -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From luojc at plum.lsc.pku.edu.cn Wed Mar 26 22:55:08 2003 From: luojc at plum.lsc.pku.edu.cn (Jingchu Luo) Date: Thu, 27 Mar 2003 06:55:08 +0800 (CST) Subject: OT: where to download transfac database? In-Reply-To: <3E81D8C1.8000409@biol.unlp.edu.ar> Message-ID: On Wed, 26 Mar 2003, Mart?n Sarachu wrote: > Hi, > > anyone knows where to download TRANSFAC version 6 public? > In the EBI mirror the latest version is TRANSFAC 3.2 It is run by a company BioBase and you should pay 500 euro for ver 6.0 as an academic user. Pls see details at: http://www.biobase.de/pages/products/databases.html Jingchu Luo > Regards, > > martin > > From edgar_wingender at yahoo.de Thu Mar 27 08:08:00 2003 From: edgar_wingender at yahoo.de (=?iso-8859-1?q?Edgar=20Wingender?=) Date: Thu, 27 Mar 2003 09:08:00 +0100 (CET) Subject: OT: where to download transfac database? In-Reply-To: Message-ID: <20030327080800.43028.qmail@web12201.mail.yahoo.com> Dear Dr. Sarachu, TRANSFAC 6.0 Public is available online only at http://www.gene-regulation.de For downlaoding and local (internal) installation, only the Professional version is available. The yearly license fee for this version (including 4 updates per year) is 500$ or 500 Euro for academic users. Licensing is done through BIOBASE, the address being given by Jingchu Luo is correct. Best regards, Edgar Wingender. > > On Wed, 26 Mar 2003, Mart?n Sarachu wrote: > > > Hi, > > > > anyone knows where to download TRANSFAC version 6 > public? > > In the EBI mirror the latest version is TRANSFAC > 3.2 > > It is run by a company BioBase and you should pay > 500 euro for ver 6.0 > as an academic user. Pls see details at: > > http://www.biobase.de/pages/products/databases.html > > Jingchu Luo > > > Regards, > > > > martin > > > > > > > ===== Prof. Dr. Edgar Wingender Department of Bioinformatics UKG, University of Goettingen Goldschmidtstr. 1, D-37077 Goettingen phone +49(0)-551-39-14911; fax +49(0)-551-39-14914 email e.wingender at med.uni-goettingen.de __________________________________________________________________ Gesendet von Yahoo! Mail - http://mail.yahoo.de Bis zu 100 MB Speicher bei http://premiummail.yahoo.de From d.m.a.martin at dundee.ac.uk Thu Mar 27 11:31:31 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Thu, 27 Mar 2003 11:31:31 +0000 Subject: Equivalent to diverge Message-ID: Is there an EMBOSS equivalent to the GCG diverge program? ..d -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From kim at inb.uni-luebeck.de Thu Mar 27 11:59:37 2003 From: kim at inb.uni-luebeck.de (Jan T. Kim) Date: Thu, 27 Mar 2003 12:59:37 +0100 Subject: question about prophecy and profit In-Reply-To: ; from janef_23@hotmail.com on Wed, Mar 26, 2003 at 03:21:26PM +0000 References: Message-ID: <20030327125937.B6130@pc10.inb.mu-luebeck.de> On Wed, Mar 26, 2003 at 03:21:26PM +0000, Jane Fowler wrote: > I am trying to use the prophecy and profit programs to locate a > consensus sequence in a genome. I am wondering if it is possible to > use a DNA sequence or if it must be a protein sequence to create a > frequency matrix. It would be great if someone could reply. [Note: The message was in HTML only, I had to manually cut & paste it into my email editor in order to quote it. Please send plain text messages to mailing lists.] I've run into the same question some time ago and found out that, prophecy and profit do not care at all what type of sequence (amino acid or nucleotide) is processed. In fact, these programs seem to operate generically on sequences of the letters a-z, in the source, I found no indication that the programs make any specific assumptions on what these letters denote biologically. The matrices produced by prophecy have 26 columns, not 20 for the amino acids (as I originally thought before I tried counting instead of thinking... ;-) ) The bottom line is: You can use prophecy and profit on any type of sequence, but note that you'll get nonsense if your sequences contain ambiguity codes (such as R for purine, Y for pyrimidine etc.). Greetinx, Jan -- +- Jan T. Kim -------------------------------------------------------+ | *NEW* email: kim at inb.uni-luebeck.de | | *NEW* WWW: http://www.inb.uni-luebeck.de/staff/kim.html | *-----=< hierarchical systems are for files, not for humans >=-----* From gwilliam at hgmp.mrc.ac.uk Thu Mar 27 13:53:36 2003 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 27 Mar 2003 13:53:36 +0000 Subject: Equivalent to diverge References: Message-ID: <3E830260.C690C817@hgmp.mrc.ac.uk> No. David Martin wrote: > > Is there an EMBOSS equivalent to the GCG diverge program? -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From squiresb at macrogenics.com Fri Mar 28 00:06:24 2003 From: squiresb at macrogenics.com (Burke Squires) Date: Thu, 27 Mar 2003 18:06:24 -0600 Subject: FW: Lib error? In-Reply-To: Message-ID: Hello, I will be using EMBOSS through the REALbasic programming environment. In an effort to see if a bioteam.net package installation would behave better with the synchronous shell mode I installed EMBOSS in addition to my 2.6.0 compiled version. Now something is not connecting...anybody have any ideas: dyld: eprimer3 can't open library: /usr/local/lib/libgd.2.dylib (No such file or directory, errno = 2) Trace/BPT trap I tried changing my .cshrc files back but now go? Thanks! Burke -- Burke Squires Bioinformatics MacroGenics, Inc. 2600 Stemmons Freeway, Suite 210 Dallas, TX 75235 USA Work: 214-634-3000 X224 Fax: 214-634-3002 ---------------------------------------------------------------------------- This e-mail and any attachments may be confidential or legally privileged. 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