From arathi at vbi.vt.edu Wed Feb 5 16:19:22 2003 From: arathi at vbi.vt.edu (Anand Rathi) Date: 05 Feb 2003 16:19:22 -0500 Subject: 'dan' related questions Message-ID: <1044479962.411.6.camel@arathi> Hi, I am using 'dan' to plot the melting temperature of a DNA sequence(~16 kbp). What I have observed is as I decrease the Window size, the melting temperature also changes. When I make the window size 2, I get melting temperature of the range -150 degrees! I checked the original paper by Breslauer et al and also recent one by Allawi & SantaLucia. Both of them have no mention of the melting temperature being dependent on the length. Could someone please explain ? Thanks, Anand Rathi, Virginia Bioinformatics Institute From newgene at bigfoot.com Wed Feb 5 20:23:21 2003 From: newgene at bigfoot.com (clwu) Date: Wed, 05 Feb 2003 19:23:21 -0600 Subject: where to download transfac data file? Message-ID: <3E41B909.2070807@bigfoot.com> Hi, group, EMBOSS tool "tfscan" needs TRANSFAC database. However when I tried to download it following the link in tfextract document: http://transfac.gbf.de/cgi-bin/download/download.pl I couldn't download it because I don't have the permission. I counld not find it neither from their ftp server: ftp://transfac.gbf.de/pub/ . Help, please. Thank you. Cl Wu From Pranay.Bhattacharyya at cshs.org Wed Feb 5 20:34:58 2003 From: Pranay.Bhattacharyya at cshs.org (Bhattacharyya, Pranay) Date: Wed, 5 Feb 2003 17:34:58 -0800 Subject: where to download transfac data file? Message-ID: <3CFAA0108952D111A5BF00805FA6FB0F0478D062@PEDSNTAS.csmc.edu> ftp://transfac.gbf.de/pub/transfac/trp/dos/transfac.taz I think this is the URL you'll need for it. -----Original Message----- From: clwu [mailto:newgene at bigfoot.com] Sent: Wednesday, February 05, 2003 5:23 PM To: emboss at embnet.org Subject: where to download transfac data file? Hi, group, EMBOSS tool "tfscan" needs TRANSFAC database. However when I tried to download it following the link in tfextract document: http://transfac.gbf.de/cgi-bin/download/download.pl I couldn't download it because I don't have the permission. I counld not find it neither from their ftp server: ftp://transfac.gbf.de/pub/ . Help, please. Thank you. Cl Wu From Pranay.Bhattacharyya at cshs.org Wed Feb 5 20:37:34 2003 From: Pranay.Bhattacharyya at cshs.org (Bhattacharyya, Pranay) Date: Wed, 5 Feb 2003 17:37:34 -0800 Subject: where to download transfac data file? Message-ID: <3CFAA0108952D111A5BF00805FA6FB0F0478D063@PEDSNTAS.csmc.edu> Sorry. This one seems to be a newer version than the one I previously sent you. ftp://transfac.gbf.de/pub/transfac/ascii/old/tf_3.2/transfac32.tar.Z version 3.3 and 3.4 doesn't look to be available from their website. I wonder why they removed it. Hope this helps. Pranay -----Original Message----- From: clwu [mailto:newgene at bigfoot.com] Sent: Wednesday, February 05, 2003 5:23 PM To: emboss at embnet.org Subject: where to download transfac data file? Hi, group, EMBOSS tool "tfscan" needs TRANSFAC database. However when I tried to download it following the link in tfextract document: http://transfac.gbf.de/cgi-bin/download/download.pl I couldn't download it because I don't have the permission. I counld not find it neither from their ftp server: ftp://transfac.gbf.de/pub/ . Help, please. Thank you. Cl Wu From sylvain.foisy at bioneq.qc.ca Wed Feb 5 20:40:37 2003 From: sylvain.foisy at bioneq.qc.ca (Sylvain Foisy) Date: Wed, 5 Feb 2003 17:40:37 -0800 Subject: where to download transfac data file? In-Reply-To: <3CFAA0108952D111A5BF00805FA6FB0F0478D063@PEDSNTAS.csmc.edu> Message-ID: Hi, On Mercredi, f?vrier 5, 2003, at 05:37 , Bhattacharyya, Pranay wrote: > Sorry. > This one seems to be a newer version than the one I previously sent you. > ftp://transfac.gbf.de/pub/transfac/ascii/old/tf_3.2/transfac32.tar.Z > > version 3.3 and 3.4 doesn't look to be available from their website. > I wonder why they removed it. From what I remember, it because it is a commercial product now. Bummer... Sylvain ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Sylvain Foisy, Ph. D. Directeur-Operations / Project Manager BioNEQ - Le Reseau quebecois de bioinformatique Universite de Montreal/Genome-Quebec 1260 Crescent, Bureau 201 Montreal, QC Tel.: (514) 878-9911 E-mail: sylvain.foisy at bioneq.qc.ca ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From sylvain.foisy at bioneq.qc.ca Wed Feb 5 20:47:44 2003 From: sylvain.foisy at bioneq.qc.ca (Sylvain Foisy) Date: Wed, 5 Feb 2003 17:47:44 -0800 Subject: where to download transfac data file? In-Reply-To: <3CFAA0108952D111A5BF00805FA6FB0F0478D064@PEDSNTAS.csmc.edu> Message-ID: hi, On Mercredi, f?vrier 5, 2003, at 05:42 , Bhattacharyya, Pranay wrote: > Ah that would be it. Thanks Sylvain. > Doesn't it seem like a lot of our programs are moving from free to > commercial use. I wonder what that'll mean for us in the future. In the case of transfac, they do have an affordable academic license (around $600 last time I checked) and you can access it through their website. Might it be time to switch DB for transcription factors, maybe EPD (http://www.epd.isb-sib.ch/) Sylvain ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Sylvain Foisy, Ph. D. Directeur-Operations / Project Manager BioNEQ - Le Reseau quebecois de bioinformatique Universite de Montreal/Genome-Quebec 1260 Crescent, Bureau 201 Montreal, QC Tel.: (514) 878-9911 E-mail: sylvain.foisy at bioneq.qc.ca ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From amauhar at tpims.org Wed Feb 5 21:26:02 2003 From: amauhar at tpims.org (America Mauhar) Date: Wed, 5 Feb 2003 18:26:02 -0800 Subject: lindna segmentation fault Message-ID: I am a new user to Emboss. I have installed (or facilitated the instalation of) Emboss 2.6 on three Mac computers running 10.2.3 (two eMacs and one powerbook of unknown vintage) and all the latest developers tools, x11 and a host of other Unix goodies. Installation seemed normal on all machines and now all machines are displaying the same behavior. Some programs are working well (transeq, wossname) but the program I really want to run, lindna, gives me "Segmentation Fault" when I try to run it from the command line and returns me to the shell prompt. Cirdna behaves in a similar manner. This is consitant for all three installations. I searched the mail group archives and found no messages relating to similar issues. Are there other OSX users successfully using this program? Thank you, America Mauhar -- -=-=-=-=-=-=-=-=-=-=-=- America Mauhar Torrey Pines Institute phone (858)455-3741 fax (858)455-3739 -=-=-=-=-=-=-=-=-=-=-=- From grsvc at mucc.mahidol.ac.th Wed Feb 5 22:57:08 2003 From: grsvc at mucc.mahidol.ac.th (Suksiri Vichasri Grams) Date: Thu, 6 Feb 2003 10:57:08 +0700 Subject: lindna segmentation fault In-Reply-To: Message-ID: <0FE83C22-3987-11D7-959F-000393629C54@mucc.mahidol.ac.th> Hi, Every Mac-user will get this error message. Alan Bleasby told me it is a problem with the default stacksize which is set too small. You must change the default value in the shell, for the sh shell the command is : ulimit -S -s unlimited; cirdna... (no typo, it is ulimit) In the tcsh shell is called : unlimit stacksize; cirdna... More info can be found in the man pages of the shells (man sh, man tcsh etc) Kindly, Rudi On Thursday, Feb 6, 2003, at 09:26 Asia/Bangkok, America Mauhar wrote: > I am a new user to Emboss. I have installed (or facilitated the > instalation of) Emboss 2.6 on three Mac computers running 10.2.3 (two > eMacs and one powerbook of unknown vintage) and all the latest > developers tools, x11 and a host of other Unix goodies. > > Installation seemed normal on all machines and now all machines are > displaying the same behavior. Some programs are working well > (transeq, wossname) but the program I really want to run, lindna, > gives me "Segmentation Fault" when I try to run it from the command > line and returns me to the shell prompt. Cirdna behaves in a similar > manner. This is consitant for all three installations. > > I searched the mail group archives and found no messages relating to > similar issues. Are there other OSX users successfully using this > program? > > Thank you, > America Mauhar > -- > -=-=-=-=-=-=-=-=-=-=-=- > America Mauhar > Torrey Pines Institute > phone (858)455-3741 > fax (858)455-3739 > -=-=-=-=-=-=-=-=-=-=-=- > > Dr. Suksiri Vichasri Grams Department of Biology Faculty of Science Mahidol University Rama VI Road Bangkok 10400 Thailand From guy at sysnet.co.il Thu Feb 6 09:50:58 2003 From: guy at sysnet.co.il (Guy Horev) Date: Thu, 6 Feb 2003 09:50:58 -0500 Subject: Windows port Message-ID: <200302061450.h16Eowte003983@sysnet.co.il> I would like to install emboss on one of the unix ports for windows, can anyone advice? Guy -- NeoMail . http://neomail.sourceforge.net From starksb at ebi.ac.uk Thu Feb 6 11:33:22 2003 From: starksb at ebi.ac.uk (David Starks-Browning) Date: Thu, 6 Feb 2003 16:33:22 +0000 Subject: Windows port In-Reply-To: <200302061450.h16Eowte003983@sysnet.co.il> References: <200302061450.h16Eowte003983@sysnet.co.il> Message-ID: <7543-Thu06Feb2003163321+0000-starksb@ebi.ac.uk> On Thursday 6 Feb 03, Guy Horev writes: > I would like to install emboss on one of the unix ports for windows, > can anyone advice? Use Cygwin from . There are some hints in the emboss list archives, if you have difficulties. Regards, David (Cygwin FAQ maintainer) ------------------------------------------------------------------- David Starks-Browning | starksb at ebi.ac.uk EMBL Outstation -- | The European Bioinformatics Institute | Wellcome Trust Genome Campus | tel: +44 (1223) 494 616 Hinxton, Cambridge, CB10 1SD, UK | fax: +44 (1223) 494 468 ------------------------------------------------------------------- From newgene at bigfoot.com Thu Feb 6 12:00:50 2003 From: newgene at bigfoot.com (clwu) Date: Thu, 06 Feb 2003 11:00:50 -0600 Subject: where to download transfac data file? References: <3CFAA0108952D111A5BF00805FA6FB0F0478D063@PEDSNTAS.csmc.edu> Message-ID: <3E4294C2.3090506@bigfoot.com> Thank you, folks, I downloaded the transfac ver3.2. I extracted it out to EMBOSS data file and ran "tfextract". "tfscan" ran OK now, but the output is different with the tfscan's document. No pattern name shown in my result. That is hard to intepret the result. I suspect it's the format problem of database file. My emboss (ver2.51) is built on cygwin/win2000. And the first several lines of my "tfvertebrate" is "HS$6-16_01\r gGGAAAaTGAAACT R00001\nHS$6-16_02\r GGGGAAAATGAAACTGCA R00002\n" (invisible chars are escaped) If it is the problem, what's the correct format? Thanks again, Cl Wu >>>>mine<<<< TFSCAN of HUMFOS from 1 to 6210 3287 3292 ttcctc 4045 4050 catgtg 3498 3503 catgtg 5590 5593 cccc 4801 4804 cccc 3239 3242 cccc 3221 3224 cccc 3150 3153 cccc 2881 2884 cccc 2089 2092 cccc 1941 1944 cccc >>>>tfscan's doc<<< TFSCAN of HSFOS from 1 to 6210 MOUSE$FCGR3A_02 R04413 3287 3292 ttcctc HS$ALBU_03 R00079 5940 5944 tggca HS$ALBU_03 R00079 3757 3761 tggca HS$ALBU_03 R00079 2776 2780 tggca HS$ALBU_03 R00079 2418 2422 tggca HS$ALBU_03 R00079 2010 2014 tggca HS$ALBU_03 R00079 1676 1680 tggca HS$ALBU_03 R00079 1356 1360 tggca HS$ALBU_02 R00078 2009 2014 ttggca Bhattacharyya, Pranay wrote: >Sorry. >This one seems to be a newer version than the one I previously sent you. >ftp://transfac.gbf.de/pub/transfac/ascii/old/tf_3.2/transfac32.tar.Z > >version 3.3 and 3.4 doesn't look to be available from their website. >I wonder why they removed it. > >Hope this helps. > >Pranay > >-----Original Message----- >From: clwu [mailto:newgene at bigfoot.com] >Sent: Wednesday, February 05, 2003 5:23 PM >To: emboss at embnet.org >Subject: where to download transfac data file? > > >Hi, group, > EMBOSS tool "tfscan" needs TRANSFAC database. However when >I tried to download it following the link in tfextract document: > >http://transfac.gbf.de/cgi-bin/download/download.pl > >I couldn't download it because I don't have the permission. > >I counld not find it neither from their ftp server: >ftp://transfac.gbf.de/pub/ . > >Help, please. > >Thank you. > > >Cl Wu > > From guy at sysnet.co.il Thu Feb 6 21:54:29 2003 From: guy at sysnet.co.il (Guy Horev) Date: Thu, 6 Feb 2003 21:54:29 -0500 Subject: Windows port Message-ID: <200302070254.h172sTiC027283@sysnet.co.il> David I managed to install EMBOSS-2.6.0 on CygWin, however I had to use the --without-x option, since make failed to create the png driver,(I installed CygWin with libpng12). I also did not succeed to install jemboss localy. Thanks in advance Guy > On Thursday 6 Feb 03, Guy Horev writes: > > I would like to install emboss on one of the unix ports for windows, > > can anyone advice? > > Use Cygwin from . There are some hints in the > emboss list archives, if you have difficulties. > > Regards, > David > (Cygwin FAQ maintainer) > > ------------------------------------------------------------------- > David Starks-Browning | starksb at ebi.ac.uk > EMBL Outstation -- | > The European Bioinformatics Institute | > Wellcome Trust Genome Campus | tel: +44 (1223) 494 616 > Hinxton, Cambridge, CB10 1SD, UK | fax: +44 (1223) 494 468 > ------------------------------------------------------------------- > > -- NeoMail . http://neomail.sourceforge.net From ald at novozymesbiotech.com Fri Feb 7 12:15:44 2003 From: ald at novozymesbiotech.com (ALLO (Alfredo Lopez De Leon)) Date: Fri, 7 Feb 2003 09:15:44 -0800 Subject: More Upgrade Message-ID: Hi, About a month ago I posted a question on how to upgrade from an early version of EMBOSS to a new release. However I got two completely opposite answers. The first stated that I should go ahead and that all my defaults databases, etc will be saved. The second one indicated that according to Alan Bleasby I will have to start from scratch. (Note: last statement was a second hand statement not done directly to me by Alan) I will appreciate it if someone can clarify this conflicting issue. I've been getting personal emails asking me if I got an answer to this problem, so I know that there are some users out there that are wondering "how to proceed". Thank you very much in advance for your help. Alfredo Lopez De Leon Ph.D. Postdoctoral Fellow, Molecular Biology and Bioinformatics Department Novozymes Biotech , Inc. 1445 Drew Avenue, Davis, CA 95616 From ableasby at hgmp.mrc.ac.uk Fri Feb 7 12:43:09 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 7 Feb 2003 17:43:09 GMT Subject: More Upgrade Message-ID: <200302071743.RAA09964@bromine.hgmp.mrc.ac.uk> You are more safe if you start from scratch. Usually you'd get away with not doing so. However, problems can arise if we move applications or ACD files between releases. It would also happen if we deleted an application (or combined functionality of two programs into one). All of these have happened. At best you may have old executables lying around. At worst it might confuse (e.g.) GUI programs into thinking non-existent programs are still there if, for instance, an unused ACD file isn't deleted. HTH Alan From asen.nenov at metalife.de Mon Feb 10 05:26:30 2003 From: asen.nenov at metalife.de (Asen Nenov) Date: Mon, 10 Feb 2003 12:26:30 +0200 Subject: CUTG ? Message-ID: <001701c2d0ee$e0e345e0$3801a8c0@metalife.bg> Hello, I am trying to setup CUTG working with EMBOSS 2.6.0. Can anyone tell me why cutgextract does not give me any signs of life? What program should I use to run CUTG db? Any help appreciated Regards Asen ------------------------------------------------------------------ METALIFE AG - Sofia, Bulgaria http://www.metalife.de asen.nenov at metalife.de ++359 2 950 1802 From isen at molbio.mgh.harvard.edu Mon Feb 10 15:17:53 2003 From: isen at molbio.mgh.harvard.edu (Thomas Isenbarger) Date: Mon, 10 Feb 2003 15:17:53 -0500 Subject: No subject Message-ID: Hello all: I have been trying to install EMBOSS on Mac OS X 10.2.3. I don't necessarily want to install support for X Windows or other graphics support. I have the new Apple X11 installed. I have tried to install the suite several times but I always seem to run into dead ends. I am fairly competent with Unix, and when I follow the instructions for doing the configure, make, and make install steps as directed, the end result is not as described in the instructions. Either the process seems to proceed as described, but the executables are not made, or I receive errors about not being able to find certain lib components or directories. Is there a guide somewhere for installing on OS X with Apple X11 installed for EMBOSS 2.6.0, both with and without the graphics libraries? Has anyone put a binary package together yet? Right now, I only want to run fuzznuc, so if I could at least get this up and running, that would be great. I don't need the whole package now, but I may eventually (graphics included). Thank-you, Tom Isenbarger -- Thomas A Isenbarger, PhD Harvard Medical School Department of Genetics Massachusetts General Hospital Department of Molecular Biology isen at molbio.mgh.harvard.edu telephone: 617/726.5973 facsimile: 617/726.6893 From arathi at vbi.vt.edu Mon Feb 10 16:09:58 2003 From: arathi at vbi.vt.edu (Anand Rathi) Date: 10 Feb 2003 16:09:58 -0500 Subject: Regd 'diffseq' Message-ID: <1044911398.371.3.camel@arathi> Hi, While using diffseq to report differences between similar sequences, I am getting the following warnings: Warning: bad /replace value 'G' Warning: bad /replace value 'G' Warning: bad /replace value 'A' Warning: bad /replace value 'A' Warning: bad /replace value 'C' Warning: bad /replace value 'G' Warning: bad /replace value 'A' Warning: bad /replace value 'G' Can somebody please elucidate the cause and fix for them. Thanks, Anand From ableasby at hgmp.mrc.ac.uk Mon Feb 10 20:10:00 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 11 Feb 2003 01:10:00 GMT Subject: Message-ID: <200302110110.BAA27539@bromine.hgmp.mrc.ac.uk> Your problem is indeed that Apple don't supply a full X11, there are no development headers etc. Other MacOSX users may be able to advise better than I on this, however I compile it on that platform using the Xfree binaries from (picking a USA mirror site for you): ftp://ftp.mirrorcentral.com/pub/XFree86/4.2.0/binaries/Darwin-ppc-5.x/ Get all the tgz files and Xinstall.sh. Then run Xinstall.sh which will unpack the tgz files and install everything. I have not tried installing it over the top of Apple's version so you'll have to consider whether you wish to clean up first. HTH Alan Bleasby HGMP From faruque at ebi.ac.uk Mon Feb 10 20:48:11 2003 From: faruque at ebi.ac.uk (Nadeem Faruque) Date: Tue, 11 Feb 2003 01:48:11 +0000 (GMT) Subject: EMBOSS on OSX X11 In-Reply-To: <200302110110.BAA27539@bromine.hgmp.mrc.ac.uk> Message-ID: I've got EMBOSS running with XFree86 in 10.1.5 (thanks to lots of help from Alan) - if you can't get anywhere with Apple's X11 have to remove it in favour of XFree86 , you should check out Adrian's OroborOSX , you'll also find help installing XFree86 there too. Having said that, are you sure that Apple's X11 is missing files - remember there's the basic X11 install, the X11 for Mac OS X Public Beta SDK (3.9MB) (see bottom right link on http://www.apple.com/macosx/x11/download/) and the normal development tools (register for a free membership at http://www.apple.com/developer/)? Nadeem On Tue, 11 Feb 2003 ableasby at hgmp.mrc.ac.uk wrote: > Your problem is indeed that Apple don't supply a full X11, there are > no development headers etc. > > Other MacOSX users may be able to advise better than I on this, > however I compile it on that platform using the Xfree binaries > from (picking a USA mirror site for you): > > ftp://ftp.mirrorcentral.com/pub/XFree86/4.2.0/binaries/Darwin-ppc-5.x/ > > Get all the tgz files and Xinstall.sh. Then run Xinstall.sh which will > unpack the tgz files and install everything. > > I have not tried installing it over the top of Apple's version so > you'll have to consider whether you wish to clean up first. > > HTH > > Alan Bleasby > HGMP > From pmr at ebi.ac.uk Tue Feb 11 04:28:12 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 11 Feb 2003 09:28:12 +0000 Subject: Regd 'diffseq' References: <1044911398.371.3.camel@arathi> Message-ID: <3E48C22C.7050305@ebi.ac.uk> Anand Rathi wrote: > While using diffseq to report differences between similar sequences, I > am getting the following warnings: > > Warning: bad /replace value 'G' > Warning: bad /replace value 'A' > Warning: bad /replace value 'C' > Can somebody please elucidate the cause and fix for them. This is a bad value ... according to the official EMBL/genBank feature table documentation: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html ... but you have to go back to version 2.2 to find this statement: /replace="change_location" where change_location is a sequence descriptor or feature name that replaces the indicated sequence to yield the difference sequence. Alternatively any valid location is acceptable and legal. The correct syntax is /replace="g" It appears you have /replace="G" in the feature table. Can you point me to the entries that are causing the problem? The check is in ajax/ajfeat.c in function featTagSpecialAllReplace However ... There are already several fixes in the checking of /replace values for known errors in EMBL/GenBank entries. This is one of them. It was fixed a week ago, so that /replace="G" (and other upper case characters, and the ambiguity codes) will be accepted by the next EMBOSS release. Some of these values will break something if we try to use them to build the "replace" sequence itself... but that is a separate problem. Diffseq will still work, but will have to report these features with note='*replace: G' rather than replace=G regards, Peter Rice From emboss_user at poczta.ibb.waw.pl Thu Feb 13 10:08:06 2003 From: emboss_user at poczta.ibb.waw.pl (Emboss User) Date: Thu, 13 Feb 2003 16:08:06 +0100 (CET) Subject: Probs with using EMBL database. Message-ID: Hello, Just directly to the point... I've installed Emboss 2.6.0 which I try to reach EMBL database from. When I try to fetch sequences using ID - everything works fine, but I'm not able to get some of sequences using their Accession Numbers. For example: % entret sptrembl:h1_chick Reads and writes (returns) flatfile entries Output file [h1_chick.entret]: % grep EMBL h1_chick.entret (...) DR EMBL; J00863; -; NOT_ANNOTATED_CDS. % entret embl:J00863 (...) Output file [e25559.entret]: ^^^^^^^^^^^^^ This is not the sequence I wanted, so lets try with ID: % grep J00863 /data/embl/acnumber.ndx (...) J00863 GGH11A1 VRT J00863 % entret embl:GGH11A1 (...) Output file [ggh11a1.entret]: % grep ID ggh11a1.entret ID GGH11A1 standard; DNA; VRT; 1098 BP. % grep AC ggh11a1.entret AC J00863; Now it is OK. It is possible to avoid searching IDs to fetch the sequence? It's not so convenient, especially from Jemboss ;) The problem is the same with any other program from Emboss, so I suspect problems in indexing. I indexed EMBL database like this: % dbiflat -idformat embl -directory ./ -filenames "*.dat" -dbname embl -release 73.0 -date 13/02/03 There is such a line in my emboss.default: DB embl [ type: N method: emblcd format: embl dir: /data/embl file: "*.dat" release: 73.0 comment: "EMBL release 73.0" ] Sorry for longish mail, I'm new to this list. Please - give me an wise advise ;) Best Regards, Grzegorz Wieczorek From Francois.Delmotte at uv.es Fri Feb 14 03:50:10 2003 From: Francois.Delmotte at uv.es (Delmotte Fran=?US-ASCII?Q?=E7?=ois) Date: Fri, 14 Feb 2003 09:50:10 +0100 (CET) Subject: EMBASSY : PHYLIP install Message-ID: <6887249923delfran@uv.es> After installing EMBOSS-2.6.0, I tried to install PHILIP-3.573c (intalla is made in /usr/local/EMBOSS-2.6.0/PHYLIP-3.573c under linux RH8) : but I could not achieve the installation correctly (problem with finding some ajax files, see below)... Can somebody please provide an advice ? Fran?ois Delmotte ----------------- Here is what I get: [root at mopusv91 PHYLIP-3.573c]# ./configure (this worked fine) .. [root at mopus PHYLIP-3.573c]# make Making all in src make[1]: enter the directory `/usr/local/EMBOSS-2.6.0/PHYLIP-3.573c/src' if gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"PHYLIP\" -DVERSION=\"3.573c\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBM=1 -I. -I. -I../include -I../../../ajax -g -O2 -MT clique.o -MD -MP -MF ".deps/clique.Tpo" \ -c -o clique.o `test -f 'clique.c' || echo './'`clique.c; \ then mv ".deps/clique.Tpo" ".deps/clique.Po"; \ else rm -f ".deps/clique.Tpo"; exit 1; \ fi clique.c:2:18: ajax.h: no such file or directory clique.c: Dans la fonction ? emboss_getoptions ?: clique.c:73: ? AjStatus ? non d?clar? (premi?re utilisation dans cette fonction) clique.c:73: (Chaque identificateur non d?clar? est rapport? une seule fois clique.c:73: pour chaque fonction dans laquelle il appara?t.) clique.c:73: erreur d'analyse syntaxique avant ? retval ? clique.c:74: ? AjPFile ? non d?clar? (premi?re utilisation dans cette fonction) clique.c:77: ? retval ? non d?clar? (premi?re utilisation dans cette fonction) clique.c:79: ? outf ? non d?clar? (premi?re utilisation dans cette fonction) clique.c:83: ? inf ? non d?clar? (premi?re utilisation dans cette fonction) clique.c:96: ? treef ? non d?clar? (premi?re utilisation dans cette fonction) make[1]: *** [clique.o] Erreur 1 make[1]: exit the directory `/usr/local/EMBOSS-2.6.0/PHYLIP-3.573c/src' make: *** [all-recursive] Erreur 1 [root at mopus PHYLIP-3.573c]# From mb4 at sanger.ac.uk Tue Feb 18 08:29:29 2003 From: mb4 at sanger.ac.uk (Matt Berriman) Date: Tue, 18 Feb 2003 13:29:29 +0000 Subject: TESTCODE Message-ID: <3E523539.1020901@sanger.ac.uk> Hi can yopu please tell me, what is the EMBOSS equivalent of GCG's TESTCODE? thanks Matt -- Dr Matthew Berriman Senior Computer Biologist - Pathogen Sequencing Unit - The Wellcome Trust Sanger Institute Tel +44 (0)1223 494817 - Fax +44 (0)1223 494919 http://www.sanger.ac.uk From fernan at iib.unsam.edu.ar Tue Feb 18 09:46:20 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Tue, 18 Feb 2003 11:46:20 -0300 Subject: TESTCODE In-Reply-To: <3E523539.1020901@sanger.ac.uk> References: <3E523539.1020901@sanger.ac.uk> Message-ID: <20030218144620.GA33436@iib.unsam.edu.ar> +----[ Matt Berriman (18.Feb.2003 10:36): | | Hi Hi Matt, | can yopu please tell me, what is the EMBOSS equivalent of GCG's TESTCODE? | thanks | Matt When I needed it I didn't find anything like this in EMBOSS, but I don't know if this functionality has been included in recent versions of EMBOSS. The testcode algorithm has been published by Fickett(1) and Paul Stothard has a Javascript version in his 'Sequence Manipulation Suite'(2). I've ported Paul's version to perl and used it succesfully. However, please note that I don't have access to GCG and can't tell if GCG's testcode produce identical results as the javascript or perl versions. (it could be possible that GCG has modified testcode after the original implementation of the Fickett algorithm). This should not be unexpected since the cutoff values to decide between coding and non-coding sequences are hard-coded in testcode and have been derived by Fickett based on a sample data set from 1982. Hope this helps, Fernan PD: I can send you the perl testcode if you want it. 1. Recognition of protein coding regions in DNA sequences. Fickett, JW (1982) Nucleic Acids Res 10(17): 5303 2. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Stothard, P (2000) BioTechniques 28: 1102 | | -- | | Dr Matthew Berriman | Senior Computer Biologist - Pathogen Sequencing Unit - | The Wellcome Trust Sanger Institute | Tel +44 (0)1223 494817 - Fax +44 (0)1223 494919 | http://www.sanger.ac.uk | +----] -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From guy at sysnet.co.il Tue Feb 18 17:22:49 2003 From: guy at sysnet.co.il (Guy Horev) Date: Tue, 18 Feb 2003 17:22:49 -0500 Subject: Help with Luke's EMBOSS_GUI Message-ID: <200302182222.h1IMMn95023383@sysnet.co.il> Hey All I'm trying to install Luke's EMBOSS_GUI on cygwin and get the output below, where can I get Mail::Mailer? Guy Writing Makefile for EMBOSS::ACD Manifying blib/man3/EMBOSS.ACD.3 Installing /usr/man/man3/EMBOSS.ACD.3 Writing /usr/lib/perl5/site_perl/5.6.1/cygwin-multi/auto/EMBOSS/ACD/.packlist Appending installation info to /usr/lib/perl5/5.6.1/cygwin-multi/perllocal.pod Warning: prerequisite Mail::Mailer failed to load: Can't locate Mail/Mailer.pm i n @INC (@INC contains: /usr/lib/perl5/5.6.1/cygwin-multi /usr/lib/perl5/5.6.1 /u sr/lib/perl5/site_perl/5.6.1/cygwin-multi /usr/lib/perl5/site_perl/5.6.1 /usr/li b/perl5/site_perl .) at (eval 7) line 3. Writing Makefile for EMBOSS::GUI Manifying blib/man3/EMBOSS.GUI.3 Manifying blib/man3/EMBOSS.GUI.3 Installing /usr/man/man3/EMBOSS.GUI.3 Writing /usr/lib/perl5/site_perl/5.6.1/cygwin-multi/auto/EMBOSS/GUI/.packlist Appending installation info to /usr/lib/perl5/5.6.1/cygwin-multi/perllocal.pod /usr/bin/perl postamble.pl /usr/bin/perl Can't locate Mail/Mailer.pm in @INC (@INC contains: /usr/lib/perl5/5.6.1/cygwin- multi /usr/lib/perl5/5.6.1 /usr/lib/perl5/site_perl/5.6.1/cygwin-multi /usr/lib/ perl5/site_perl/5.6.1 /usr/lib/perl5/site_perl .) at /usr/lib/perl5/site_perl/5. 6.1/EMBOSS/GUI.pm line 95. BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.6.1/EMBOSS/GUI.p m line 95. Compilation failed in require at postamble.pl line 4. BEGIN failed--compilation aborted at postamble.pl line 4. make: *** [postamble] Error 2 -- NeoMail . http://neomail.sourceforge.net From mccarthy at cs.usask.ca Tue Feb 18 20:53:55 2003 From: mccarthy at cs.usask.ca (Luke McCarthy) Date: 18 Feb 2003 19:53:55 -0600 Subject: Help with Luke's EMBOSS_GUI Message-ID: <1045619634.1617.20.camel@kerouac> On Tue, 18 Feb 2003, Guy Horev wrote: > Hey All > > I'm trying to install Luke's EMBOSS_GUI on cygwin and get the output > below, where can I get Mail::Mailer? Mail::Mailer is just an everyday, ordinary CPAN module. If you've used CPAN before, the following should work (from a shell prompt) perl -MCPAN -e 'install Mail::Mailer' If you've not used CPAN before, the above should still work, it will just take longer and you'll have to answer a few questions. I've never used this method under cygwin either, so your mileage may vary. The nice thing about using the perl CPAN interface is that it will automatically figure out dependencies and pull in other required modules. I'm not sure if Mail::Mailer requires anything else or not. If you have to (or just want to) install Mail::Mailer manually, you can download it from http://search.cpan.org/src/MARKOV/MailTools-1.58/Mail/Mailer.pm and stick it somewhere in your perl module path. For more information, see the CPAN FAQ at http://www.cpan.org/misc/cpan-faq.html, particularly the questions 'Where can I find Perl modules?' and 'How do I install Perl modules?' Cheers, Luke -- Luke McCarthy Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan mccarthy at cs.usask.ca From yezq at mail.cbi.pku.edu.cn Thu Feb 20 01:23:57 2003 From: yezq at mail.cbi.pku.edu.cn (Zhiqiang Ye) Date: Thu, 20 Feb 2003 14:23:57 +0800 Subject: about jemboss.properties Message-ID: <200302200601.h1K61Oj21324@mail.cbi.pku.edu.cn> Dear all, Because my clustalw's path has changed,I have to modify this line---in the file " jemboss.properties " at this line : embossPath=......... but emma doesn't work. What should I do to let this line take effect? Thanks ! ???? ???????????????? Best Regards! ????????????????????????????Zhiqiang Ye ????????????????????????????yezq at mail.cbi.pku.edu.cn ??????????????????????????????????2003-02-20 ############################################################### Zhiqiang Ye, Ph. D candidate, Major in Bioinformatics Center of BioInformatics, College of Life Scicences, Peking University, Beijing, PR China 100871 E-mail: yezq at mail.cbi.pku.edu.cn , yezhiqiang at ccermail.net URL: http://www.cbi.pku.edu.cn Tel: +86 10 6275 6730 ############################################################### From ftcheung at hkusua.hku.hk Fri Feb 21 04:07:11 2003 From: ftcheung at hkusua.hku.hk (Frankie Cheung) Date: Fri, 21 Feb 2003 17:07:11 +0800 (HKT) Subject: Problem when building database index Message-ID: Dear Sir/Madam, Can anyone help me? I don't know how to build database index in EMBOSS for the following databanks as I can't find any related information from the administration manual: - PDB - OGLYC - BLOCKS - PFAM - PRODOM - TAXONOMY - ENZYME - dbEST - dbSTS - dbGSS - dbSNP (XML format now: would EMBOSS consider to allow build XML db index in next version ?) - UNIGENE - LocusLink - OMIM - InterPro Thanks for your attention. Frankie Cheung From pmr at ebi.ac.uk Fri Feb 21 04:24:17 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 21 Feb 2003 09:24:17 +0000 Subject: Problem when building database index References: Message-ID: <3E55F041.4090505@ebi.ac.uk> Frankie Cheung wrote: > Can anyone help me? I don't know how to build database index in EMBOSS > for the following databanks as I can't find any related information > from the administration manual: Some of these are not sequence databases - but I do plan to add nmore database types in the near future (I already started to extend the emboss.default syntax for them) > - PDB The domainatrix EMBASSY package uses cleaned PDB files. Do you want the sequences or the structures? > - PFAM > - PRODOM Alignment databases are high on my list of things to do. One (small) problem is how to name the individual sequences in an alignment, for example in a PFAM entry. > - OGLYC > - BLOCKS > - TAXONOMY > - ENZYME How would you use these in EMBOSS? Or do you just want to use them with entret (entret is only for sequences, but we can make a general version) > - dbEST > - dbSTS > - dbGSS These are available as FASTA format files (so you can use dbifasta) - or you can index the huge flatfile versions with SRS and use the SRSFASTA access method (which asks SRS to write the sequence in FASTA format, and then reads it into EMBOSS) > - dbSNP (XML format now: would EMBOSS consider to allow build XML db > index in next version ?) Yes, we will consider XML format databases - but how would you use dbSNP entries in EMBOSS? > - UNIGENE The UNIGENE clusters are available as "almost" fasta files (they have headers for each cluster). You can index in SRS and use the SRSFASTA access method. I am looking at skipping the headers and allowing dbifasta to index these files directly - but there is a choice of clusters (see pfam above) or single sequences as "entries". In SRS the UNIGENE data can be nidexed in both ways. > - LocusLink How would you use this in EMBOSS? > - OMIM > - InterPro Ah, XML again! In progress. Does anyone else have requests for databases under EMBOSS to help set priorities for this work? Hope this helps, Peter From Stephan.Hurling at evotecoai.com Fri Feb 21 11:15:44 2003 From: Stephan.Hurling at evotecoai.com (Stephan.Hurling at evotecoai.com) Date: Fri, 21 Feb 2003 17:15:44 +0100 Subject: How to extract feature protein_id out of GCG genbank databases? Message-ID: Hello, I would like to index GCG genebank databases in a way, that I will also index the protein id, stored as an additional information in the features section for a sequence: GCG database entry: ... COMMENT On Oct 14, 1999 this sequence version replaced ... FEATURES Location/Qualifiers source 1. .1839 /organism="Homo sapiens" CDS 165. .1448 .......... ---> /protein_id="AAC123456" ... Current emboss entrys, dumped with "seqret -osformat debug" for a sequence show no available features: ... Features: 'No' ... Can someone give ma a hint, how to include the protein id in my indices? How do I have to change the call to "dbigcg"? I would like to be able to use "whichdb 'protein_id' "for locating the specific protein in the connected databases. Thanks in advance. All the best, Stephan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030221/fc1676ff/attachment.html From d.m.a.martin at dundee.ac.uk Tue Feb 25 05:13:07 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Tue, 25 Feb 2003 10:13:07 +0000 Subject: Multiple reports for an application Message-ID: Having started to use the rformat options, is it possible to generate more than one format for a particular program. ie, if I am running fuzzpro and would like not only a listfile but also the motif output do I have to runthe analysis twice or can EMBOSS ouptput multiple reports in different formats? ..d -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From pmr at ebi.ac.uk Tue Feb 25 05:44:23 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 25 Feb 2003 10:44:23 +0000 Subject: Multiple reports for an application References: Message-ID: <3E5B4907.4040502@ebi.ac.uk> David Martin wrote: > Having started to use the rformat options, is it possible to generate more > than one format for a particular program. > > ie, if I am running fuzzpro and would like not only a listfile but also the > motif output do I have to run the analysis twice or can EMBOSS output > multiple reports in different formats? You need to run the program twice. Producing two report formats is trivial (two calls to the report writing code with different formats), but where would you write the second report? An alternative is to save the report in rformat GFF and rewrite the features (demoreport does this kind of thing) but it would need a way to specify the report columns for some of the reports... unless, perhaps, we can save them in a GFF header comment. Hmmmm .... could be interesting. Still very tricky for reports on more than one sequence, if any format needs to report the sequence. But worth think about some more. Hope this helps, Peter From d.m.a.martin at dundee.ac.uk Tue Feb 25 06:07:23 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Tue, 25 Feb 2003 11:07:23 +0000 Subject: Multiple reports for an application In-Reply-To: <3E5B4907.4040502@ebi.ac.uk> Message-ID: On 25/2/03 10:44 am, "Peter Rice" wrote: > David Martin wrote: >> Having started to use the rformat options, is it possible to generate more >> than one format for a particular program. >> >> ie, if I am running fuzzpro and would like not only a listfile but also the >> motif output do I have to run the analysis twice or can EMBOSS output >> multiple reports in different formats? > > You need to run the program twice. > > Producing two report formats is trivial (two calls to the report writing > code with different formats), but where would you write the second report? -routfile gives the base so -rformat gff,listfile -routfile report should give report.gff and report.listfile A thought. ..d > > An alternative is to save the report in rformat GFF and rewrite the > features (demoreport does this kind of thing) but it would need a way to > specify the report columns for some of the reports... unless, perhaps, > we can save them in a GFF header comment. Hmmmm .... could be > interesting. Still very tricky for reports on more than one sequence, if > any format needs to report the sequence. But worth think about some more. > > Hope this helps, > > Peter > > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From pmr at ebi.ac.uk Tue Feb 25 06:28:23 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 25 Feb 2003 11:28:23 +0000 Subject: Multiple reports for an application References: Message-ID: <3E5B5357.1010600@ebi.ac.uk> David Martin wrote: > -routfile gives the base so > > -rformat gff,listfile -routfile report > > should give > report.gff and report.listfile Sorry, (1) the qualifier is -rname and (2) it makes the output file report.fuzzpro for both reports!!! I think the GFF file intermediate may work - I will try extending demoreport to do this. Peter From aengus.stewart at cancer.org.uk Tue Feb 25 12:00:31 2003 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Tue, 25 Feb 2003 17:00:31 +0000 Subject: possible buglet seqret? Message-ID: <3E5BA12F.2D452930@cancer.org.uk> Hi, I am just now setting up database access by EMBOSS ( yes late on the scene as usual ) as I have undated to EMBOSS 2.6 Currently I still have to run GCG in parallel :-( with EMBOSS so for my testset I have been using GCG formatted swissnew. I have the following definition in my emboss.default After formatting When I run seqret -feature -osf swiss I dont get the feature table in the resultant output file if the feature table is only one line! eg swissnew:6pgd_mouse - 1 line FT DOESNT work swissnew:3bp5_human - 2 line FT DOES work swissnew:143c_arath - 1 line FT DOESNT work swissnew:27aa_arath - 2 line FT DOES work I also tried with getting the raw data and using dbiflat instead of dbigcg with the same results. Regards Aengus -- -------------------------------------------------------------------------- Aengus Stewart aengus.stewart at cancer.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 gbottu at black.vub.ac.be Thu Feb 27 08:16:56 2003 From: gbottu at black.vub.ac.be (Guy Bottu) Date: Thu, 27 Feb 2003 14:16:56 +0100 Subject: EMBOSS+SwissProt+Prosite on public server, problem ??? Message-ID: <20030227141656.A1137339@black.vub.ac.be> from : Belgian EMBnet Node Dear colleagues, This concerns EMBnet Nodes and others who have external users. The CIB is getting concerned about access to SwissProt and Prosite by industrial users who did not pay a licence to the CIB. You have perhaps just like us received a note requesting to provide information about access by industrial users. I would be happy to hear your opinion about this matter. - providing information : If use is limited to registered users running programs under a UNIX user name and EMBOSS logging is on, it is easy to see who is using Prosite (those running patmatdb). I however see no (easy) way to check who is using SwissProt (we access SwissProt by getz for "Single"/"Query" and by direct reading of a fastA format db for "All" mode) - limiting access : the note did not mention limiting access, although they might request it later. I think a possibility is to create a UNIX user group with all the academic and licenced industrial users and make SwissProt and Prosite only readable by this group. Regards, Guy Bottu From jrvalverde at cnb.uam.es Thu Feb 27 09:16:34 2003 From: jrvalverde at cnb.uam.es (José R. Valverde) Date: Thu, 27 Feb 2003 15:16:34 +0100 Subject: EMBOSS+SwissProt+Prosite on public server, problem ??? In-Reply-To: <20030227141656.A1137339@black.vub.ac.be> References: <20030227141656.A1137339@black.vub.ac.be> Message-ID: <20030227151634.60cb3d1f.jrvalverde@cnb.uam.es> Methinks that SP people started by relying on good faith for commercial users who were expected to abide by the license and now suspect very high levels of "piracy" through the public servers. As for the logs.. that's a tough one, because it will reveal information about users, and NOW we are required (in EU at least) to protect it (unless users agree first). Again, this was not a real concern when SP started their licensing, since law was fuzzy, and no one knew what to do, but things are different now. So, logs are probably out of question unless all accesses logged required PREVIOUSLY an explicit acceptance from users of such log disposal/redistribution to SP. An alternative that wouldn't reveal much user data would be to pick up connecting site names and send a list to SP people. But I can't be sure it would be legal either. The problem, as I see it, is that by producing those old logs now, we may be breaking the law. OTOH, if SP suspects unlawful conduct from companies, they must first try to get an injunction to request the logs. But we are speaking of international law here, and that is costly. To be fair, SP guys are our friends, we are as interested as them in their success, we NEED them, as much as they need us, and we don't want to make things difficult for them. But we can't break the law either. So, what I would suggest is this: I suppose that if SP didn't bring this up earlier, it's because it wasn't a problem from them, it's now that they are concerned. So, from now on, we may do like with GCG, i.e. either only give access to academic users or shield access behind an online licensing screen which displays SwissProt License, states clearly that logs MAY be sent to them and requires acceptance before granting access. Then, from now on, we would all be on the safe side and ready to cooperate and profit mutually. Speaking of me: while I had registered commercial users, I kept both the latest release and the latest _free_ release, and produced a note stating that commercial users needed a license. But I never required them to state their acceptance to me, nor to agree on my giving away any of their data. I guess I can't produce logs now. But I willfully could do it in the future if SP guys feel it will help them, by modifying the access procedures. j From david at cnb.uam.es Thu Feb 27 12:01:02 2003 From: david at cnb.uam.es (David Garcia Aristegui) Date: Thu, 27 Feb 2003 18:01:02 +0100 Subject: AIX installation question Message-ID: We have problems compiling the EMBOSS 2.6.0 release in a AIX 5 ( using gcc 3.2.2 compiler ). The error with make: make[1] *** No rule to make target `.deps/yank.Po`. Stop. Please, can anybody help us ( with configure details etc etc )?, thank you very much. From ableasby at hgmp.mrc.ac.uk Thu Feb 27 12:53:30 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 27 Feb 2003 17:53:30 GMT Subject: AIX installation question Message-ID: <200302271753.RAA21752@bromine.hgmp.mrc.ac.uk> AIX grep is limited as far as line length is concerned. You will get that error (amongst others) if "which grep" shows /usr/bin/grep. You should install GNU grep and make sure it appears in your path before the system-supplied grep. It would then be best if you did a rm -rf EMBOSS-2.6.0 and start again from an untar of the distribution (existing .deps directories might throw a spanner in the works even if you reconfigured your failed source). Finally, I've never tried GNU C under AIX, the configuration is really designed for the xlc compiler on that system. To pick that compiler up (assuming its installed) you should make sure /usr/vac/bin is in your path and type: setenv CC xlc (or sh equivalent) before configuring. Alan From fernan at iib.unsam.edu.ar Fri Feb 28 13:50:01 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Fri, 28 Feb 2003 15:50:01 -0300 Subject: pick sequencing primers to cover a whole sequence Message-ID: <20030228185001.GG84954@iib.unsam.edu.ar> Is there an app within emboss that would allow me to pick sequencing primers to cover a whole sequence? Say I have a sequence of 3-5 Kb that I want to sequence completely. I want to place primers each one separated around 400 bp on each strand. I can do this manually, but what if I have a reasonable number of this kind of sequences? I'd like to use a primer design program to discard primers with loops, hairpins, poor 3' ends, etc. and also to produce primers compatible with automated sequencing conditions. Perhaps someone can point me to an external program, if emboss currently doesn't carry any with this functionality. Or perhaps I can fool primer3 by tweaking some parameters? Thanks in advance, Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From ccloa at mdlab.com Fri Feb 28 16:25:55 2003 From: ccloa at mdlab.com (Chien-Chang Loa) Date: Fri, 28 Feb 2003 16:25:55 -0500 Subject: question about EMMA program Message-ID: <388BFAA4-4B63-11D7-A393-000393A9E5CC@mdlab.com> Dear: I tried to do some alignment of multiple sequences with the program EMMA. However, I could not get the input of multiple sequences recognized by the EMMA. Does anyone know how to establish a sequence file with extension as ".pep" or make a List file as suggested by the instruction of EMMA program? The instruction suggested text editor pico or nedit. Does anyone know where can we get this kind of text editor? Do you think the regular Microsoft Word software will work for editing the sequence file or the List file for multiple sequences?? How can we input the sequences from NCBI directly to the EMMA or other programs of the EMBOSS? I tried the accession numbers but did not work. Does anyone know how to get the similarity table and phylogenetic tree with any of the software program in the EMBOSS? I think you already know that I am new with these programs of EMBOSS. Any help or suggestions from you will be very appreciated. Thanks. Chien-Chang Loa From arathi at vbi.vt.edu Wed Feb 5 21:19:22 2003 From: arathi at vbi.vt.edu (Anand Rathi) Date: 05 Feb 2003 16:19:22 -0500 Subject: 'dan' related questions Message-ID: <1044479962.411.6.camel@arathi> Hi, I am using 'dan' to plot the melting temperature of a DNA sequence(~16 kbp). What I have observed is as I decrease the Window size, the melting temperature also changes. When I make the window size 2, I get melting temperature of the range -150 degrees! I checked the original paper by Breslauer et al and also recent one by Allawi & SantaLucia. Both of them have no mention of the melting temperature being dependent on the length. Could someone please explain ? Thanks, Anand Rathi, Virginia Bioinformatics Institute From newgene at bigfoot.com Thu Feb 6 01:23:21 2003 From: newgene at bigfoot.com (clwu) Date: Wed, 05 Feb 2003 19:23:21 -0600 Subject: where to download transfac data file? Message-ID: <3E41B909.2070807@bigfoot.com> Hi, group, EMBOSS tool "tfscan" needs TRANSFAC database. However when I tried to download it following the link in tfextract document: http://transfac.gbf.de/cgi-bin/download/download.pl I couldn't download it because I don't have the permission. I counld not find it neither from their ftp server: ftp://transfac.gbf.de/pub/ . Help, please. Thank you. Cl Wu From Pranay.Bhattacharyya at cshs.org Thu Feb 6 01:34:58 2003 From: Pranay.Bhattacharyya at cshs.org (Bhattacharyya, Pranay) Date: Wed, 5 Feb 2003 17:34:58 -0800 Subject: where to download transfac data file? Message-ID: <3CFAA0108952D111A5BF00805FA6FB0F0478D062@PEDSNTAS.csmc.edu> ftp://transfac.gbf.de/pub/transfac/trp/dos/transfac.taz I think this is the URL you'll need for it. -----Original Message----- From: clwu [mailto:newgene at bigfoot.com] Sent: Wednesday, February 05, 2003 5:23 PM To: emboss at embnet.org Subject: where to download transfac data file? Hi, group, EMBOSS tool "tfscan" needs TRANSFAC database. However when I tried to download it following the link in tfextract document: http://transfac.gbf.de/cgi-bin/download/download.pl I couldn't download it because I don't have the permission. I counld not find it neither from their ftp server: ftp://transfac.gbf.de/pub/ . Help, please. Thank you. Cl Wu From Pranay.Bhattacharyya at cshs.org Thu Feb 6 01:37:34 2003 From: Pranay.Bhattacharyya at cshs.org (Bhattacharyya, Pranay) Date: Wed, 5 Feb 2003 17:37:34 -0800 Subject: where to download transfac data file? Message-ID: <3CFAA0108952D111A5BF00805FA6FB0F0478D063@PEDSNTAS.csmc.edu> Sorry. This one seems to be a newer version than the one I previously sent you. ftp://transfac.gbf.de/pub/transfac/ascii/old/tf_3.2/transfac32.tar.Z version 3.3 and 3.4 doesn't look to be available from their website. I wonder why they removed it. Hope this helps. Pranay -----Original Message----- From: clwu [mailto:newgene at bigfoot.com] Sent: Wednesday, February 05, 2003 5:23 PM To: emboss at embnet.org Subject: where to download transfac data file? Hi, group, EMBOSS tool "tfscan" needs TRANSFAC database. However when I tried to download it following the link in tfextract document: http://transfac.gbf.de/cgi-bin/download/download.pl I couldn't download it because I don't have the permission. I counld not find it neither from their ftp server: ftp://transfac.gbf.de/pub/ . Help, please. Thank you. Cl Wu From sylvain.foisy at bioneq.qc.ca Thu Feb 6 01:40:37 2003 From: sylvain.foisy at bioneq.qc.ca (Sylvain Foisy) Date: Wed, 5 Feb 2003 17:40:37 -0800 Subject: where to download transfac data file? In-Reply-To: <3CFAA0108952D111A5BF00805FA6FB0F0478D063@PEDSNTAS.csmc.edu> Message-ID: Hi, On Mercredi, f?vrier 5, 2003, at 05:37 , Bhattacharyya, Pranay wrote: > Sorry. > This one seems to be a newer version than the one I previously sent you. > ftp://transfac.gbf.de/pub/transfac/ascii/old/tf_3.2/transfac32.tar.Z > > version 3.3 and 3.4 doesn't look to be available from their website. > I wonder why they removed it. From what I remember, it because it is a commercial product now. Bummer... Sylvain ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Sylvain Foisy, Ph. D. Directeur-Operations / Project Manager BioNEQ - Le Reseau quebecois de bioinformatique Universite de Montreal/Genome-Quebec 1260 Crescent, Bureau 201 Montreal, QC Tel.: (514) 878-9911 E-mail: sylvain.foisy at bioneq.qc.ca ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From sylvain.foisy at bioneq.qc.ca Thu Feb 6 01:47:44 2003 From: sylvain.foisy at bioneq.qc.ca (Sylvain Foisy) Date: Wed, 5 Feb 2003 17:47:44 -0800 Subject: where to download transfac data file? In-Reply-To: <3CFAA0108952D111A5BF00805FA6FB0F0478D064@PEDSNTAS.csmc.edu> Message-ID: hi, On Mercredi, f?vrier 5, 2003, at 05:42 , Bhattacharyya, Pranay wrote: > Ah that would be it. Thanks Sylvain. > Doesn't it seem like a lot of our programs are moving from free to > commercial use. I wonder what that'll mean for us in the future. In the case of transfac, they do have an affordable academic license (around $600 last time I checked) and you can access it through their website. Might it be time to switch DB for transcription factors, maybe EPD (http://www.epd.isb-sib.ch/) Sylvain ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Sylvain Foisy, Ph. D. Directeur-Operations / Project Manager BioNEQ - Le Reseau quebecois de bioinformatique Universite de Montreal/Genome-Quebec 1260 Crescent, Bureau 201 Montreal, QC Tel.: (514) 878-9911 E-mail: sylvain.foisy at bioneq.qc.ca ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From amauhar at tpims.org Thu Feb 6 02:26:02 2003 From: amauhar at tpims.org (America Mauhar) Date: Wed, 5 Feb 2003 18:26:02 -0800 Subject: lindna segmentation fault Message-ID: I am a new user to Emboss. I have installed (or facilitated the instalation of) Emboss 2.6 on three Mac computers running 10.2.3 (two eMacs and one powerbook of unknown vintage) and all the latest developers tools, x11 and a host of other Unix goodies. Installation seemed normal on all machines and now all machines are displaying the same behavior. Some programs are working well (transeq, wossname) but the program I really want to run, lindna, gives me "Segmentation Fault" when I try to run it from the command line and returns me to the shell prompt. Cirdna behaves in a similar manner. This is consitant for all three installations. I searched the mail group archives and found no messages relating to similar issues. Are there other OSX users successfully using this program? Thank you, America Mauhar -- -=-=-=-=-=-=-=-=-=-=-=- America Mauhar Torrey Pines Institute phone (858)455-3741 fax (858)455-3739 -=-=-=-=-=-=-=-=-=-=-=- From grsvc at mucc.mahidol.ac.th Thu Feb 6 03:57:08 2003 From: grsvc at mucc.mahidol.ac.th (Suksiri Vichasri Grams) Date: Thu, 6 Feb 2003 10:57:08 +0700 Subject: lindna segmentation fault In-Reply-To: Message-ID: <0FE83C22-3987-11D7-959F-000393629C54@mucc.mahidol.ac.th> Hi, Every Mac-user will get this error message. Alan Bleasby told me it is a problem with the default stacksize which is set too small. You must change the default value in the shell, for the sh shell the command is : ulimit -S -s unlimited; cirdna... (no typo, it is ulimit) In the tcsh shell is called : unlimit stacksize; cirdna... More info can be found in the man pages of the shells (man sh, man tcsh etc) Kindly, Rudi On Thursday, Feb 6, 2003, at 09:26 Asia/Bangkok, America Mauhar wrote: > I am a new user to Emboss. I have installed (or facilitated the > instalation of) Emboss 2.6 on three Mac computers running 10.2.3 (two > eMacs and one powerbook of unknown vintage) and all the latest > developers tools, x11 and a host of other Unix goodies. > > Installation seemed normal on all machines and now all machines are > displaying the same behavior. Some programs are working well > (transeq, wossname) but the program I really want to run, lindna, > gives me "Segmentation Fault" when I try to run it from the command > line and returns me to the shell prompt. Cirdna behaves in a similar > manner. This is consitant for all three installations. > > I searched the mail group archives and found no messages relating to > similar issues. Are there other OSX users successfully using this > program? > > Thank you, > America Mauhar > -- > -=-=-=-=-=-=-=-=-=-=-=- > America Mauhar > Torrey Pines Institute > phone (858)455-3741 > fax (858)455-3739 > -=-=-=-=-=-=-=-=-=-=-=- > > Dr. Suksiri Vichasri Grams Department of Biology Faculty of Science Mahidol University Rama VI Road Bangkok 10400 Thailand From guy at sysnet.co.il Thu Feb 6 14:50:58 2003 From: guy at sysnet.co.il (Guy Horev) Date: Thu, 6 Feb 2003 09:50:58 -0500 Subject: Windows port Message-ID: <200302061450.h16Eowte003983@sysnet.co.il> I would like to install emboss on one of the unix ports for windows, can anyone advice? Guy -- NeoMail . http://neomail.sourceforge.net From starksb at ebi.ac.uk Thu Feb 6 16:33:22 2003 From: starksb at ebi.ac.uk (David Starks-Browning) Date: Thu, 6 Feb 2003 16:33:22 +0000 Subject: Windows port In-Reply-To: <200302061450.h16Eowte003983@sysnet.co.il> References: <200302061450.h16Eowte003983@sysnet.co.il> Message-ID: <7543-Thu06Feb2003163321+0000-starksb@ebi.ac.uk> On Thursday 6 Feb 03, Guy Horev writes: > I would like to install emboss on one of the unix ports for windows, > can anyone advice? Use Cygwin from . There are some hints in the emboss list archives, if you have difficulties. Regards, David (Cygwin FAQ maintainer) ------------------------------------------------------------------- David Starks-Browning | starksb at ebi.ac.uk EMBL Outstation -- | The European Bioinformatics Institute | Wellcome Trust Genome Campus | tel: +44 (1223) 494 616 Hinxton, Cambridge, CB10 1SD, UK | fax: +44 (1223) 494 468 ------------------------------------------------------------------- From newgene at bigfoot.com Thu Feb 6 17:00:50 2003 From: newgene at bigfoot.com (clwu) Date: Thu, 06 Feb 2003 11:00:50 -0600 Subject: where to download transfac data file? References: <3CFAA0108952D111A5BF00805FA6FB0F0478D063@PEDSNTAS.csmc.edu> Message-ID: <3E4294C2.3090506@bigfoot.com> Thank you, folks, I downloaded the transfac ver3.2. I extracted it out to EMBOSS data file and ran "tfextract". "tfscan" ran OK now, but the output is different with the tfscan's document. No pattern name shown in my result. That is hard to intepret the result. I suspect it's the format problem of database file. My emboss (ver2.51) is built on cygwin/win2000. And the first several lines of my "tfvertebrate" is "HS$6-16_01\r gGGAAAaTGAAACT R00001\nHS$6-16_02\r GGGGAAAATGAAACTGCA R00002\n" (invisible chars are escaped) If it is the problem, what's the correct format? Thanks again, Cl Wu >>>>mine<<<< TFSCAN of HUMFOS from 1 to 6210 3287 3292 ttcctc 4045 4050 catgtg 3498 3503 catgtg 5590 5593 cccc 4801 4804 cccc 3239 3242 cccc 3221 3224 cccc 3150 3153 cccc 2881 2884 cccc 2089 2092 cccc 1941 1944 cccc >>>>tfscan's doc<<< TFSCAN of HSFOS from 1 to 6210 MOUSE$FCGR3A_02 R04413 3287 3292 ttcctc HS$ALBU_03 R00079 5940 5944 tggca HS$ALBU_03 R00079 3757 3761 tggca HS$ALBU_03 R00079 2776 2780 tggca HS$ALBU_03 R00079 2418 2422 tggca HS$ALBU_03 R00079 2010 2014 tggca HS$ALBU_03 R00079 1676 1680 tggca HS$ALBU_03 R00079 1356 1360 tggca HS$ALBU_02 R00078 2009 2014 ttggca Bhattacharyya, Pranay wrote: >Sorry. >This one seems to be a newer version than the one I previously sent you. >ftp://transfac.gbf.de/pub/transfac/ascii/old/tf_3.2/transfac32.tar.Z > >version 3.3 and 3.4 doesn't look to be available from their website. >I wonder why they removed it. > >Hope this helps. > >Pranay > >-----Original Message----- >From: clwu [mailto:newgene at bigfoot.com] >Sent: Wednesday, February 05, 2003 5:23 PM >To: emboss at embnet.org >Subject: where to download transfac data file? > > >Hi, group, > EMBOSS tool "tfscan" needs TRANSFAC database. However when >I tried to download it following the link in tfextract document: > >http://transfac.gbf.de/cgi-bin/download/download.pl > >I couldn't download it because I don't have the permission. > >I counld not find it neither from their ftp server: >ftp://transfac.gbf.de/pub/ . > >Help, please. > >Thank you. > > >Cl Wu > > From guy at sysnet.co.il Fri Feb 7 02:54:29 2003 From: guy at sysnet.co.il (Guy Horev) Date: Thu, 6 Feb 2003 21:54:29 -0500 Subject: Windows port Message-ID: <200302070254.h172sTiC027283@sysnet.co.il> David I managed to install EMBOSS-2.6.0 on CygWin, however I had to use the --without-x option, since make failed to create the png driver,(I installed CygWin with libpng12). I also did not succeed to install jemboss localy. Thanks in advance Guy > On Thursday 6 Feb 03, Guy Horev writes: > > I would like to install emboss on one of the unix ports for windows, > > can anyone advice? > > Use Cygwin from . There are some hints in the > emboss list archives, if you have difficulties. > > Regards, > David > (Cygwin FAQ maintainer) > > ------------------------------------------------------------------- > David Starks-Browning | starksb at ebi.ac.uk > EMBL Outstation -- | > The European Bioinformatics Institute | > Wellcome Trust Genome Campus | tel: +44 (1223) 494 616 > Hinxton, Cambridge, CB10 1SD, UK | fax: +44 (1223) 494 468 > ------------------------------------------------------------------- > > -- NeoMail . http://neomail.sourceforge.net From ald at novozymesbiotech.com Fri Feb 7 17:15:44 2003 From: ald at novozymesbiotech.com (ALLO (Alfredo Lopez De Leon)) Date: Fri, 7 Feb 2003 09:15:44 -0800 Subject: More Upgrade Message-ID: Hi, About a month ago I posted a question on how to upgrade from an early version of EMBOSS to a new release. However I got two completely opposite answers. The first stated that I should go ahead and that all my defaults databases, etc will be saved. The second one indicated that according to Alan Bleasby I will have to start from scratch. (Note: last statement was a second hand statement not done directly to me by Alan) I will appreciate it if someone can clarify this conflicting issue. I've been getting personal emails asking me if I got an answer to this problem, so I know that there are some users out there that are wondering "how to proceed". Thank you very much in advance for your help. Alfredo Lopez De Leon Ph.D. Postdoctoral Fellow, Molecular Biology and Bioinformatics Department Novozymes Biotech , Inc. 1445 Drew Avenue, Davis, CA 95616 From ableasby at hgmp.mrc.ac.uk Fri Feb 7 17:43:09 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 7 Feb 2003 17:43:09 GMT Subject: More Upgrade Message-ID: <200302071743.RAA09964@bromine.hgmp.mrc.ac.uk> You are more safe if you start from scratch. Usually you'd get away with not doing so. However, problems can arise if we move applications or ACD files between releases. It would also happen if we deleted an application (or combined functionality of two programs into one). All of these have happened. At best you may have old executables lying around. At worst it might confuse (e.g.) GUI programs into thinking non-existent programs are still there if, for instance, an unused ACD file isn't deleted. HTH Alan From asen.nenov at metalife.de Mon Feb 10 10:26:30 2003 From: asen.nenov at metalife.de (Asen Nenov) Date: Mon, 10 Feb 2003 12:26:30 +0200 Subject: CUTG ? Message-ID: <001701c2d0ee$e0e345e0$3801a8c0@metalife.bg> Hello, I am trying to setup CUTG working with EMBOSS 2.6.0. Can anyone tell me why cutgextract does not give me any signs of life? What program should I use to run CUTG db? Any help appreciated Regards Asen ------------------------------------------------------------------ METALIFE AG - Sofia, Bulgaria http://www.metalife.de asen.nenov at metalife.de ++359 2 950 1802 From isen at molbio.mgh.harvard.edu Mon Feb 10 20:17:53 2003 From: isen at molbio.mgh.harvard.edu (Thomas Isenbarger) Date: Mon, 10 Feb 2003 15:17:53 -0500 Subject: No subject Message-ID: Hello all: I have been trying to install EMBOSS on Mac OS X 10.2.3. I don't necessarily want to install support for X Windows or other graphics support. I have the new Apple X11 installed. I have tried to install the suite several times but I always seem to run into dead ends. I am fairly competent with Unix, and when I follow the instructions for doing the configure, make, and make install steps as directed, the end result is not as described in the instructions. Either the process seems to proceed as described, but the executables are not made, or I receive errors about not being able to find certain lib components or directories. Is there a guide somewhere for installing on OS X with Apple X11 installed for EMBOSS 2.6.0, both with and without the graphics libraries? Has anyone put a binary package together yet? Right now, I only want to run fuzznuc, so if I could at least get this up and running, that would be great. I don't need the whole package now, but I may eventually (graphics included). Thank-you, Tom Isenbarger -- Thomas A Isenbarger, PhD Harvard Medical School Department of Genetics Massachusetts General Hospital Department of Molecular Biology isen at molbio.mgh.harvard.edu telephone: 617/726.5973 facsimile: 617/726.6893 From arathi at vbi.vt.edu Mon Feb 10 21:09:58 2003 From: arathi at vbi.vt.edu (Anand Rathi) Date: 10 Feb 2003 16:09:58 -0500 Subject: Regd 'diffseq' Message-ID: <1044911398.371.3.camel@arathi> Hi, While using diffseq to report differences between similar sequences, I am getting the following warnings: Warning: bad /replace value 'G' Warning: bad /replace value 'G' Warning: bad /replace value 'A' Warning: bad /replace value 'A' Warning: bad /replace value 'C' Warning: bad /replace value 'G' Warning: bad /replace value 'A' Warning: bad /replace value 'G' Can somebody please elucidate the cause and fix for them. Thanks, Anand From ableasby at hgmp.mrc.ac.uk Tue Feb 11 01:10:00 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 11 Feb 2003 01:10:00 GMT Subject: Message-ID: <200302110110.BAA27539@bromine.hgmp.mrc.ac.uk> Your problem is indeed that Apple don't supply a full X11, there are no development headers etc. Other MacOSX users may be able to advise better than I on this, however I compile it on that platform using the Xfree binaries from (picking a USA mirror site for you): ftp://ftp.mirrorcentral.com/pub/XFree86/4.2.0/binaries/Darwin-ppc-5.x/ Get all the tgz files and Xinstall.sh. Then run Xinstall.sh which will unpack the tgz files and install everything. I have not tried installing it over the top of Apple's version so you'll have to consider whether you wish to clean up first. HTH Alan Bleasby HGMP From faruque at ebi.ac.uk Tue Feb 11 01:48:11 2003 From: faruque at ebi.ac.uk (Nadeem Faruque) Date: Tue, 11 Feb 2003 01:48:11 +0000 (GMT) Subject: EMBOSS on OSX X11 In-Reply-To: <200302110110.BAA27539@bromine.hgmp.mrc.ac.uk> Message-ID: I've got EMBOSS running with XFree86 in 10.1.5 (thanks to lots of help from Alan) - if you can't get anywhere with Apple's X11 have to remove it in favour of XFree86 , you should check out Adrian's OroborOSX , you'll also find help installing XFree86 there too. Having said that, are you sure that Apple's X11 is missing files - remember there's the basic X11 install, the X11 for Mac OS X Public Beta SDK (3.9MB) (see bottom right link on http://www.apple.com/macosx/x11/download/) and the normal development tools (register for a free membership at http://www.apple.com/developer/)? Nadeem On Tue, 11 Feb 2003 ableasby at hgmp.mrc.ac.uk wrote: > Your problem is indeed that Apple don't supply a full X11, there are > no development headers etc. > > Other MacOSX users may be able to advise better than I on this, > however I compile it on that platform using the Xfree binaries > from (picking a USA mirror site for you): > > ftp://ftp.mirrorcentral.com/pub/XFree86/4.2.0/binaries/Darwin-ppc-5.x/ > > Get all the tgz files and Xinstall.sh. Then run Xinstall.sh which will > unpack the tgz files and install everything. > > I have not tried installing it over the top of Apple's version so > you'll have to consider whether you wish to clean up first. > > HTH > > Alan Bleasby > HGMP > From pmr at ebi.ac.uk Tue Feb 11 09:28:12 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 11 Feb 2003 09:28:12 +0000 Subject: Regd 'diffseq' References: <1044911398.371.3.camel@arathi> Message-ID: <3E48C22C.7050305@ebi.ac.uk> Anand Rathi wrote: > While using diffseq to report differences between similar sequences, I > am getting the following warnings: > > Warning: bad /replace value 'G' > Warning: bad /replace value 'A' > Warning: bad /replace value 'C' > Can somebody please elucidate the cause and fix for them. This is a bad value ... according to the official EMBL/genBank feature table documentation: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html ... but you have to go back to version 2.2 to find this statement: /replace="change_location" where change_location is a sequence descriptor or feature name that replaces the indicated sequence to yield the difference sequence. Alternatively any valid location is acceptable and legal. The correct syntax is /replace="g" It appears you have /replace="G" in the feature table. Can you point me to the entries that are causing the problem? The check is in ajax/ajfeat.c in function featTagSpecialAllReplace However ... There are already several fixes in the checking of /replace values for known errors in EMBL/GenBank entries. This is one of them. It was fixed a week ago, so that /replace="G" (and other upper case characters, and the ambiguity codes) will be accepted by the next EMBOSS release. Some of these values will break something if we try to use them to build the "replace" sequence itself... but that is a separate problem. Diffseq will still work, but will have to report these features with note='*replace: G' rather than replace=G regards, Peter Rice From emboss_user at poczta.ibb.waw.pl Thu Feb 13 15:08:06 2003 From: emboss_user at poczta.ibb.waw.pl (Emboss User) Date: Thu, 13 Feb 2003 16:08:06 +0100 (CET) Subject: Probs with using EMBL database. Message-ID: Hello, Just directly to the point... I've installed Emboss 2.6.0 which I try to reach EMBL database from. When I try to fetch sequences using ID - everything works fine, but I'm not able to get some of sequences using their Accession Numbers. For example: % entret sptrembl:h1_chick Reads and writes (returns) flatfile entries Output file [h1_chick.entret]: % grep EMBL h1_chick.entret (...) DR EMBL; J00863; -; NOT_ANNOTATED_CDS. % entret embl:J00863 (...) Output file [e25559.entret]: ^^^^^^^^^^^^^ This is not the sequence I wanted, so lets try with ID: % grep J00863 /data/embl/acnumber.ndx (...) J00863 GGH11A1 VRT J00863 % entret embl:GGH11A1 (...) Output file [ggh11a1.entret]: % grep ID ggh11a1.entret ID GGH11A1 standard; DNA; VRT; 1098 BP. % grep AC ggh11a1.entret AC J00863; Now it is OK. It is possible to avoid searching IDs to fetch the sequence? It's not so convenient, especially from Jemboss ;) The problem is the same with any other program from Emboss, so I suspect problems in indexing. I indexed EMBL database like this: % dbiflat -idformat embl -directory ./ -filenames "*.dat" -dbname embl -release 73.0 -date 13/02/03 There is such a line in my emboss.default: DB embl [ type: N method: emblcd format: embl dir: /data/embl file: "*.dat" release: 73.0 comment: "EMBL release 73.0" ] Sorry for longish mail, I'm new to this list. Please - give me an wise advise ;) Best Regards, Grzegorz Wieczorek From Francois.Delmotte at uv.es Fri Feb 14 08:50:10 2003 From: Francois.Delmotte at uv.es (Delmotte Fran=?US-ASCII?Q?=E7?=ois) Date: Fri, 14 Feb 2003 09:50:10 +0100 (CET) Subject: EMBASSY : PHYLIP install Message-ID: <6887249923delfran@uv.es> After installing EMBOSS-2.6.0, I tried to install PHILIP-3.573c (intalla is made in /usr/local/EMBOSS-2.6.0/PHYLIP-3.573c under linux RH8) : but I could not achieve the installation correctly (problem with finding some ajax files, see below)... Can somebody please provide an advice ? Fran?ois Delmotte ----------------- Here is what I get: [root at mopusv91 PHYLIP-3.573c]# ./configure (this worked fine) .. [root at mopus PHYLIP-3.573c]# make Making all in src make[1]: enter the directory `/usr/local/EMBOSS-2.6.0/PHYLIP-3.573c/src' if gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"PHYLIP\" -DVERSION=\"3.573c\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBM=1 -I. -I. -I../include -I../../../ajax -g -O2 -MT clique.o -MD -MP -MF ".deps/clique.Tpo" \ -c -o clique.o `test -f 'clique.c' || echo './'`clique.c; \ then mv ".deps/clique.Tpo" ".deps/clique.Po"; \ else rm -f ".deps/clique.Tpo"; exit 1; \ fi clique.c:2:18: ajax.h: no such file or directory clique.c: Dans la fonction ? emboss_getoptions ?: clique.c:73: ? AjStatus ? non d?clar? (premi?re utilisation dans cette fonction) clique.c:73: (Chaque identificateur non d?clar? est rapport? une seule fois clique.c:73: pour chaque fonction dans laquelle il appara?t.) clique.c:73: erreur d'analyse syntaxique avant ? retval ? clique.c:74: ? AjPFile ? non d?clar? (premi?re utilisation dans cette fonction) clique.c:77: ? retval ? non d?clar? (premi?re utilisation dans cette fonction) clique.c:79: ? outf ? non d?clar? (premi?re utilisation dans cette fonction) clique.c:83: ? inf ? non d?clar? (premi?re utilisation dans cette fonction) clique.c:96: ? treef ? non d?clar? (premi?re utilisation dans cette fonction) make[1]: *** [clique.o] Erreur 1 make[1]: exit the directory `/usr/local/EMBOSS-2.6.0/PHYLIP-3.573c/src' make: *** [all-recursive] Erreur 1 [root at mopus PHYLIP-3.573c]# From mb4 at sanger.ac.uk Tue Feb 18 13:29:29 2003 From: mb4 at sanger.ac.uk (Matt Berriman) Date: Tue, 18 Feb 2003 13:29:29 +0000 Subject: TESTCODE Message-ID: <3E523539.1020901@sanger.ac.uk> Hi can yopu please tell me, what is the EMBOSS equivalent of GCG's TESTCODE? thanks Matt -- Dr Matthew Berriman Senior Computer Biologist - Pathogen Sequencing Unit - The Wellcome Trust Sanger Institute Tel +44 (0)1223 494817 - Fax +44 (0)1223 494919 http://www.sanger.ac.uk From fernan at iib.unsam.edu.ar Tue Feb 18 14:46:20 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Tue, 18 Feb 2003 11:46:20 -0300 Subject: TESTCODE In-Reply-To: <3E523539.1020901@sanger.ac.uk> References: <3E523539.1020901@sanger.ac.uk> Message-ID: <20030218144620.GA33436@iib.unsam.edu.ar> +----[ Matt Berriman (18.Feb.2003 10:36): | | Hi Hi Matt, | can yopu please tell me, what is the EMBOSS equivalent of GCG's TESTCODE? | thanks | Matt When I needed it I didn't find anything like this in EMBOSS, but I don't know if this functionality has been included in recent versions of EMBOSS. The testcode algorithm has been published by Fickett(1) and Paul Stothard has a Javascript version in his 'Sequence Manipulation Suite'(2). I've ported Paul's version to perl and used it succesfully. However, please note that I don't have access to GCG and can't tell if GCG's testcode produce identical results as the javascript or perl versions. (it could be possible that GCG has modified testcode after the original implementation of the Fickett algorithm). This should not be unexpected since the cutoff values to decide between coding and non-coding sequences are hard-coded in testcode and have been derived by Fickett based on a sample data set from 1982. Hope this helps, Fernan PD: I can send you the perl testcode if you want it. 1. Recognition of protein coding regions in DNA sequences. Fickett, JW (1982) Nucleic Acids Res 10(17): 5303 2. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Stothard, P (2000) BioTechniques 28: 1102 | | -- | | Dr Matthew Berriman | Senior Computer Biologist - Pathogen Sequencing Unit - | The Wellcome Trust Sanger Institute | Tel +44 (0)1223 494817 - Fax +44 (0)1223 494919 | http://www.sanger.ac.uk | +----] -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From guy at sysnet.co.il Tue Feb 18 22:22:49 2003 From: guy at sysnet.co.il (Guy Horev) Date: Tue, 18 Feb 2003 17:22:49 -0500 Subject: Help with Luke's EMBOSS_GUI Message-ID: <200302182222.h1IMMn95023383@sysnet.co.il> Hey All I'm trying to install Luke's EMBOSS_GUI on cygwin and get the output below, where can I get Mail::Mailer? Guy Writing Makefile for EMBOSS::ACD Manifying blib/man3/EMBOSS.ACD.3 Installing /usr/man/man3/EMBOSS.ACD.3 Writing /usr/lib/perl5/site_perl/5.6.1/cygwin-multi/auto/EMBOSS/ACD/.packlist Appending installation info to /usr/lib/perl5/5.6.1/cygwin-multi/perllocal.pod Warning: prerequisite Mail::Mailer failed to load: Can't locate Mail/Mailer.pm i n @INC (@INC contains: /usr/lib/perl5/5.6.1/cygwin-multi /usr/lib/perl5/5.6.1 /u sr/lib/perl5/site_perl/5.6.1/cygwin-multi /usr/lib/perl5/site_perl/5.6.1 /usr/li b/perl5/site_perl .) at (eval 7) line 3. Writing Makefile for EMBOSS::GUI Manifying blib/man3/EMBOSS.GUI.3 Manifying blib/man3/EMBOSS.GUI.3 Installing /usr/man/man3/EMBOSS.GUI.3 Writing /usr/lib/perl5/site_perl/5.6.1/cygwin-multi/auto/EMBOSS/GUI/.packlist Appending installation info to /usr/lib/perl5/5.6.1/cygwin-multi/perllocal.pod /usr/bin/perl postamble.pl /usr/bin/perl Can't locate Mail/Mailer.pm in @INC (@INC contains: /usr/lib/perl5/5.6.1/cygwin- multi /usr/lib/perl5/5.6.1 /usr/lib/perl5/site_perl/5.6.1/cygwin-multi /usr/lib/ perl5/site_perl/5.6.1 /usr/lib/perl5/site_perl .) at /usr/lib/perl5/site_perl/5. 6.1/EMBOSS/GUI.pm line 95. BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.6.1/EMBOSS/GUI.p m line 95. Compilation failed in require at postamble.pl line 4. BEGIN failed--compilation aborted at postamble.pl line 4. make: *** [postamble] Error 2 -- NeoMail . http://neomail.sourceforge.net From mccarthy at cs.usask.ca Wed Feb 19 01:53:55 2003 From: mccarthy at cs.usask.ca (Luke McCarthy) Date: 18 Feb 2003 19:53:55 -0600 Subject: Help with Luke's EMBOSS_GUI Message-ID: <1045619634.1617.20.camel@kerouac> On Tue, 18 Feb 2003, Guy Horev wrote: > Hey All > > I'm trying to install Luke's EMBOSS_GUI on cygwin and get the output > below, where can I get Mail::Mailer? Mail::Mailer is just an everyday, ordinary CPAN module. If you've used CPAN before, the following should work (from a shell prompt) perl -MCPAN -e 'install Mail::Mailer' If you've not used CPAN before, the above should still work, it will just take longer and you'll have to answer a few questions. I've never used this method under cygwin either, so your mileage may vary. The nice thing about using the perl CPAN interface is that it will automatically figure out dependencies and pull in other required modules. I'm not sure if Mail::Mailer requires anything else or not. If you have to (or just want to) install Mail::Mailer manually, you can download it from http://search.cpan.org/src/MARKOV/MailTools-1.58/Mail/Mailer.pm and stick it somewhere in your perl module path. For more information, see the CPAN FAQ at http://www.cpan.org/misc/cpan-faq.html, particularly the questions 'Where can I find Perl modules?' and 'How do I install Perl modules?' Cheers, Luke -- Luke McCarthy Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan mccarthy at cs.usask.ca From yezq at mail.cbi.pku.edu.cn Thu Feb 20 06:23:57 2003 From: yezq at mail.cbi.pku.edu.cn (Zhiqiang Ye) Date: Thu, 20 Feb 2003 14:23:57 +0800 Subject: about jemboss.properties Message-ID: <200302200601.h1K61Oj21324@mail.cbi.pku.edu.cn> Dear all, Because my clustalw's path has changed,I have to modify this line---in the file " jemboss.properties " at this line : embossPath=......... but emma doesn't work. What should I do to let this line take effect? Thanks ! ?? ???????? Best Regards! ??????????????Zhiqiang Ye ??????????????yezq at mail.cbi.pku.edu.cn ?????????????????2003-02-20 ############################################################### Zhiqiang Ye, Ph. D candidate, Major in Bioinformatics Center of BioInformatics, College of Life Scicences, Peking University, Beijing, PR China 100871 E-mail: yezq at mail.cbi.pku.edu.cn , yezhiqiang at ccermail.net URL: http://www.cbi.pku.edu.cn Tel: +86 10 6275 6730 ############################################################### From ftcheung at hkusua.hku.hk Fri Feb 21 09:07:11 2003 From: ftcheung at hkusua.hku.hk (Frankie Cheung) Date: Fri, 21 Feb 2003 17:07:11 +0800 (HKT) Subject: Problem when building database index Message-ID: Dear Sir/Madam, Can anyone help me? I don't know how to build database index in EMBOSS for the following databanks as I can't find any related information from the administration manual: - PDB - OGLYC - BLOCKS - PFAM - PRODOM - TAXONOMY - ENZYME - dbEST - dbSTS - dbGSS - dbSNP (XML format now: would EMBOSS consider to allow build XML db index in next version ?) - UNIGENE - LocusLink - OMIM - InterPro Thanks for your attention. Frankie Cheung From pmr at ebi.ac.uk Fri Feb 21 09:24:17 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 21 Feb 2003 09:24:17 +0000 Subject: Problem when building database index References: Message-ID: <3E55F041.4090505@ebi.ac.uk> Frankie Cheung wrote: > Can anyone help me? I don't know how to build database index in EMBOSS > for the following databanks as I can't find any related information > from the administration manual: Some of these are not sequence databases - but I do plan to add nmore database types in the near future (I already started to extend the emboss.default syntax for them) > - PDB The domainatrix EMBASSY package uses cleaned PDB files. Do you want the sequences or the structures? > - PFAM > - PRODOM Alignment databases are high on my list of things to do. One (small) problem is how to name the individual sequences in an alignment, for example in a PFAM entry. > - OGLYC > - BLOCKS > - TAXONOMY > - ENZYME How would you use these in EMBOSS? Or do you just want to use them with entret (entret is only for sequences, but we can make a general version) > - dbEST > - dbSTS > - dbGSS These are available as FASTA format files (so you can use dbifasta) - or you can index the huge flatfile versions with SRS and use the SRSFASTA access method (which asks SRS to write the sequence in FASTA format, and then reads it into EMBOSS) > - dbSNP (XML format now: would EMBOSS consider to allow build XML db > index in next version ?) Yes, we will consider XML format databases - but how would you use dbSNP entries in EMBOSS? > - UNIGENE The UNIGENE clusters are available as "almost" fasta files (they have headers for each cluster). You can index in SRS and use the SRSFASTA access method. I am looking at skipping the headers and allowing dbifasta to index these files directly - but there is a choice of clusters (see pfam above) or single sequences as "entries". In SRS the UNIGENE data can be nidexed in both ways. > - LocusLink How would you use this in EMBOSS? > - OMIM > - InterPro Ah, XML again! In progress. Does anyone else have requests for databases under EMBOSS to help set priorities for this work? Hope this helps, Peter From Stephan.Hurling at evotecoai.com Fri Feb 21 16:15:44 2003 From: Stephan.Hurling at evotecoai.com (Stephan.Hurling at evotecoai.com) Date: Fri, 21 Feb 2003 17:15:44 +0100 Subject: How to extract feature protein_id out of GCG genbank databases? Message-ID: Hello, I would like to index GCG genebank databases in a way, that I will also index the protein id, stored as an additional information in the features section for a sequence: GCG database entry: ... COMMENT On Oct 14, 1999 this sequence version replaced ... FEATURES Location/Qualifiers source 1. .1839 /organism="Homo sapiens" CDS 165. .1448 .......... ---> /protein_id="AAC123456" ... Current emboss entrys, dumped with "seqret -osformat debug" for a sequence show no available features: ... Features: 'No' ... Can someone give ma a hint, how to include the protein id in my indices? How do I have to change the call to "dbigcg"? I would like to be able to use "whichdb 'protein_id' "for locating the specific protein in the connected databases. Thanks in advance. All the best, Stephan -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.m.a.martin at dundee.ac.uk Tue Feb 25 10:13:07 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Tue, 25 Feb 2003 10:13:07 +0000 Subject: Multiple reports for an application Message-ID: Having started to use the rformat options, is it possible to generate more than one format for a particular program. ie, if I am running fuzzpro and would like not only a listfile but also the motif output do I have to runthe analysis twice or can EMBOSS ouptput multiple reports in different formats? ..d -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From pmr at ebi.ac.uk Tue Feb 25 10:44:23 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 25 Feb 2003 10:44:23 +0000 Subject: Multiple reports for an application References: Message-ID: <3E5B4907.4040502@ebi.ac.uk> David Martin wrote: > Having started to use the rformat options, is it possible to generate more > than one format for a particular program. > > ie, if I am running fuzzpro and would like not only a listfile but also the > motif output do I have to run the analysis twice or can EMBOSS output > multiple reports in different formats? You need to run the program twice. Producing two report formats is trivial (two calls to the report writing code with different formats), but where would you write the second report? An alternative is to save the report in rformat GFF and rewrite the features (demoreport does this kind of thing) but it would need a way to specify the report columns for some of the reports... unless, perhaps, we can save them in a GFF header comment. Hmmmm .... could be interesting. Still very tricky for reports on more than one sequence, if any format needs to report the sequence. But worth think about some more. Hope this helps, Peter From d.m.a.martin at dundee.ac.uk Tue Feb 25 11:07:23 2003 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Tue, 25 Feb 2003 11:07:23 +0000 Subject: Multiple reports for an application In-Reply-To: <3E5B4907.4040502@ebi.ac.uk> Message-ID: On 25/2/03 10:44 am, "Peter Rice" wrote: > David Martin wrote: >> Having started to use the rformat options, is it possible to generate more >> than one format for a particular program. >> >> ie, if I am running fuzzpro and would like not only a listfile but also the >> motif output do I have to run the analysis twice or can EMBOSS output >> multiple reports in different formats? > > You need to run the program twice. > > Producing two report formats is trivial (two calls to the report writing > code with different formats), but where would you write the second report? -routfile gives the base so -rformat gff,listfile -routfile report should give report.gff and report.listfile A thought. ..d > > An alternative is to save the report in rformat GFF and rewrite the > features (demoreport does this kind of thing) but it would need a way to > specify the report columns for some of the reports... unless, perhaps, > we can save them in a GFF header comment. Hmmmm .... could be > interesting. Still very tricky for reports on more than one sequence, if > any format needs to report the sequence. But worth think about some more. > > Hope this helps, > > Peter > > -- David Martin PhD Bioinformatics Scientific Officer Post-Genomics and Molecular Interactions Centre University of Dundee From pmr at ebi.ac.uk Tue Feb 25 11:28:23 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 25 Feb 2003 11:28:23 +0000 Subject: Multiple reports for an application References: Message-ID: <3E5B5357.1010600@ebi.ac.uk> David Martin wrote: > -routfile gives the base so > > -rformat gff,listfile -routfile report > > should give > report.gff and report.listfile Sorry, (1) the qualifier is -rname and (2) it makes the output file report.fuzzpro for both reports!!! I think the GFF file intermediate may work - I will try extending demoreport to do this. Peter From aengus.stewart at cancer.org.uk Tue Feb 25 17:00:31 2003 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Tue, 25 Feb 2003 17:00:31 +0000 Subject: possible buglet seqret? Message-ID: <3E5BA12F.2D452930@cancer.org.uk> Hi, I am just now setting up database access by EMBOSS ( yes late on the scene as usual ) as I have undated to EMBOSS 2.6 Currently I still have to run GCG in parallel :-( with EMBOSS so for my testset I have been using GCG formatted swissnew. I have the following definition in my emboss.default After formatting When I run seqret -feature -osf swiss I dont get the feature table in the resultant output file if the feature table is only one line! eg swissnew:6pgd_mouse - 1 line FT DOESNT work swissnew:3bp5_human - 2 line FT DOES work swissnew:143c_arath - 1 line FT DOESNT work swissnew:27aa_arath - 2 line FT DOES work I also tried with getting the raw data and using dbiflat instead of dbigcg with the same results. Regards Aengus -- -------------------------------------------------------------------------- Aengus Stewart aengus.stewart at cancer.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 gbottu at black.vub.ac.be Thu Feb 27 13:16:56 2003 From: gbottu at black.vub.ac.be (Guy Bottu) Date: Thu, 27 Feb 2003 14:16:56 +0100 Subject: EMBOSS+SwissProt+Prosite on public server, problem ??? Message-ID: <20030227141656.A1137339@black.vub.ac.be> from : Belgian EMBnet Node Dear colleagues, This concerns EMBnet Nodes and others who have external users. The CIB is getting concerned about access to SwissProt and Prosite by industrial users who did not pay a licence to the CIB. You have perhaps just like us received a note requesting to provide information about access by industrial users. I would be happy to hear your opinion about this matter. - providing information : If use is limited to registered users running programs under a UNIX user name and EMBOSS logging is on, it is easy to see who is using Prosite (those running patmatdb). I however see no (easy) way to check who is using SwissProt (we access SwissProt by getz for "Single"/"Query" and by direct reading of a fastA format db for "All" mode) - limiting access : the note did not mention limiting access, although they might request it later. I think a possibility is to create a UNIX user group with all the academic and licenced industrial users and make SwissProt and Prosite only readable by this group. Regards, Guy Bottu From jrvalverde at cnb.uam.es Thu Feb 27 14:16:34 2003 From: jrvalverde at cnb.uam.es (José R. Valverde) Date: Thu, 27 Feb 2003 15:16:34 +0100 Subject: EMBOSS+SwissProt+Prosite on public server, problem ??? In-Reply-To: <20030227141656.A1137339@black.vub.ac.be> References: <20030227141656.A1137339@black.vub.ac.be> Message-ID: <20030227151634.60cb3d1f.jrvalverde@cnb.uam.es> Methinks that SP people started by relying on good faith for commercial users who were expected to abide by the license and now suspect very high levels of "piracy" through the public servers. As for the logs.. that's a tough one, because it will reveal information about users, and NOW we are required (in EU at least) to protect it (unless users agree first). Again, this was not a real concern when SP started their licensing, since law was fuzzy, and no one knew what to do, but things are different now. So, logs are probably out of question unless all accesses logged required PREVIOUSLY an explicit acceptance from users of such log disposal/redistribution to SP. An alternative that wouldn't reveal much user data would be to pick up connecting site names and send a list to SP people. But I can't be sure it would be legal either. The problem, as I see it, is that by producing those old logs now, we may be breaking the law. OTOH, if SP suspects unlawful conduct from companies, they must first try to get an injunction to request the logs. But we are speaking of international law here, and that is costly. To be fair, SP guys are our friends, we are as interested as them in their success, we NEED them, as much as they need us, and we don't want to make things difficult for them. But we can't break the law either. So, what I would suggest is this: I suppose that if SP didn't bring this up earlier, it's because it wasn't a problem from them, it's now that they are concerned. So, from now on, we may do like with GCG, i.e. either only give access to academic users or shield access behind an online licensing screen which displays SwissProt License, states clearly that logs MAY be sent to them and requires acceptance before granting access. Then, from now on, we would all be on the safe side and ready to cooperate and profit mutually. Speaking of me: while I had registered commercial users, I kept both the latest release and the latest _free_ release, and produced a note stating that commercial users needed a license. But I never required them to state their acceptance to me, nor to agree on my giving away any of their data. I guess I can't produce logs now. But I willfully could do it in the future if SP guys feel it will help them, by modifying the access procedures. j From david at cnb.uam.es Thu Feb 27 17:01:02 2003 From: david at cnb.uam.es (David Garcia Aristegui) Date: Thu, 27 Feb 2003 18:01:02 +0100 Subject: AIX installation question Message-ID: We have problems compiling the EMBOSS 2.6.0 release in a AIX 5 ( using gcc 3.2.2 compiler ). The error with make: make[1] *** No rule to make target `.deps/yank.Po`. Stop. Please, can anybody help us ( with configure details etc etc )?, thank you very much. From ableasby at hgmp.mrc.ac.uk Thu Feb 27 17:53:30 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 27 Feb 2003 17:53:30 GMT Subject: AIX installation question Message-ID: <200302271753.RAA21752@bromine.hgmp.mrc.ac.uk> AIX grep is limited as far as line length is concerned. You will get that error (amongst others) if "which grep" shows /usr/bin/grep. You should install GNU grep and make sure it appears in your path before the system-supplied grep. It would then be best if you did a rm -rf EMBOSS-2.6.0 and start again from an untar of the distribution (existing .deps directories might throw a spanner in the works even if you reconfigured your failed source). Finally, I've never tried GNU C under AIX, the configuration is really designed for the xlc compiler on that system. To pick that compiler up (assuming its installed) you should make sure /usr/vac/bin is in your path and type: setenv CC xlc (or sh equivalent) before configuring. Alan From fernan at iib.unsam.edu.ar Fri Feb 28 18:50:01 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Fri, 28 Feb 2003 15:50:01 -0300 Subject: pick sequencing primers to cover a whole sequence Message-ID: <20030228185001.GG84954@iib.unsam.edu.ar> Is there an app within emboss that would allow me to pick sequencing primers to cover a whole sequence? Say I have a sequence of 3-5 Kb that I want to sequence completely. I want to place primers each one separated around 400 bp on each strand. I can do this manually, but what if I have a reasonable number of this kind of sequences? I'd like to use a primer design program to discard primers with loops, hairpins, poor 3' ends, etc. and also to produce primers compatible with automated sequencing conditions. Perhaps someone can point me to an external program, if emboss currently doesn't carry any with this functionality. Or perhaps I can fool primer3 by tweaking some parameters? Thanks in advance, Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From ccloa at mdlab.com Fri Feb 28 21:25:55 2003 From: ccloa at mdlab.com (Chien-Chang Loa) Date: Fri, 28 Feb 2003 16:25:55 -0500 Subject: question about EMMA program Message-ID: <388BFAA4-4B63-11D7-A393-000393A9E5CC@mdlab.com> Dear: I tried to do some alignment of multiple sequences with the program EMMA. However, I could not get the input of multiple sequences recognized by the EMMA. Does anyone know how to establish a sequence file with extension as ".pep" or make a List file as suggested by the instruction of EMMA program? The instruction suggested text editor pico or nedit. Does anyone know where can we get this kind of text editor? Do you think the regular Microsoft Word software will work for editing the sequence file or the List file for multiple sequences?? How can we input the sequences from NCBI directly to the EMMA or other programs of the EMBOSS? I tried the accession numbers but did not work. Does anyone know how to get the similarity table and phylogenetic tree with any of the software program in the EMBOSS? I think you already know that I am new with these programs of EMBOSS. Any help or suggestions from you will be very appreciated. Thanks. Chien-Chang Loa