From lukem at gene.pbi.nrc.ca Thu May 2 20:44:36 2002 From: lukem at gene.pbi.nrc.ca (Luke McCarthy) Date: Thu, 2 May 2002 18:44:36 -0600 (CST) Subject: EMBOSS::GUI 1.0 Message-ID: Hi everybody, Last July I announced on this list the development of a Perl CGI graphical interface to the EMBOSS scripts and solicited beta testers. Development has been intermittent since then, but I believe the interface is now ready for public consumption. The GUI scripts generate the application pages dynamically from the EMBOSS ACD files, so it should adapt to newer EMBOSS releases without much hassle (all of the current features that I am aware of are available, including output formats for sequences, features, reports and alignments...) The main menu is generated dynamically as well, so only those tools which are available on your system will be listed (for example, if you haven't installed the EMBASSY stuff it won't show up...) The GUI can be downloaded from http://bioinfo.pbi.nrc.ca/~lukem/EMBOSS or http://www.cbr.nrc.ca/EMBOSS and a demo version is available online at http://bioinfo.pbi.nrc.ca/cgi-bin/emboss-redirect.pl Cheers, Luke McCarthy lukem at bioinfo.pbi.nrc.ca From aiyar at ebv.mimnet.northwestern.edu Thu May 2 21:50:57 2002 From: aiyar at ebv.mimnet.northwestern.edu (Ashok Aiyar) Date: Thu, 2 May 2002 20:50:57 -0500 (CDT) Subject: EMBOSS::GUI 1.0 In-Reply-To: Message-ID: On Thu, 2 May 2002, Luke McCarthy wrote: > Hi everybody, > > Last July I announced on this list the development of a Perl CGI graphical > interface to the EMBOSS scripts and solicited beta testers. Development > has been intermittent since then, but I believe the interface is now ready > for public consumption. > > The GUI can be downloaded from http://bioinfo.pbi.nrc.ca/~lukem/EMBOSS or > http://www.cbr.nrc.ca/EMBOSS and a demo version is available online at > http://bioinfo.pbi.nrc.ca/cgi-bin/emboss-redirect.pl > Can I add that my lab has been using Luke's EMBOSS-GUI for close to a year. It is really simple to install, and does provide a consistent and intuitive user-interface. Thanks Luke! Ashok -- Ashok Aiyar, Ph.D. Assistant Professor email: a-aiyar at northwestern.edu Department of Microbiology-Immunology office: (312) 503-2524 303 E. Chicago Avenue, WARD 4-123 lab: (312) 503-2542 Northwestern University, Chicago, IL 60611 fax: (312) 503-1339 From asen.nenov at metalife.de Tue May 7 09:44:08 2002 From: asen.nenov at metalife.de (Asen Nenov) Date: Tue, 07 May 2002 13:44:08 GMT Subject: unable to open font file?? Message-ID: <20020507.13440800@senski.bg> Hi to All, My EMBOSS(current version) is running on Mandrake 8.1/Duron/256. I tried all of PLOT programs, but all of the are giving me the following message: Cannot open library file: plstnd5.fnt Please set PLPLOT_LIB to the plplot/lib directory under emboss *** PLPLOT ERROR *** Unable to open font file Can anyone help me eith this issue? Any help appreciated. Best Regards Asen From dmamartin at dundee.ac.uk Tue May 7 11:39:09 2002 From: dmamartin at dundee.ac.uk (David Martin) Date: Tue, 7 May 2002 16:39:09 +0100 (BST) Subject: unable to open font file?? In-Reply-To: <20020507.13440800@senski.bg> Message-ID: On Tue, 7 May 2002, Asen Nenov wrote: > Hi to All, > > My EMBOSS(current version) is running on Mandrake 8.1/Duron/256. > I tried all of PLOT programs, but all of the are giving me the following > message: > > Cannot open library file: plstnd5.fnt > Please set PLPLOT_LIB to the plplot/lib directory under emboss > > *** PLPLOT ERROR *** > > Unable to open font file > > Can anyone help me eith this issue? > Any help appreciated. The error is somewhat misleading and is correct only if you are running from the source directory. If you have installed (with 'make install') then copy the font files plstnd5.fnt and plxtnd5.fnt to the share/EMBOSS directory (typically /usr/local/share/EMBOSS unless you have configured with --prefix=/somewhere ) You will find these files in /plplot/lib Hope this helps ..d > > Best Regards > Asen > ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee +44 1382 348704 ---------------------------------- From mathog at mendel.bio.caltech.edu Fri May 10 17:35:45 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Fri, 10 May 2002 14:35:45 -0700 Subject: seqret reading from stdin with unkown type Message-ID: I don't understand why this one fails: # ( echo "AGTTT" ; echo "ACGTTTTTGGT" ) \ | seqret -sequence=stdin -out=gcg::stdout Reads and writes (returns) sequences Error: Unable to read sequence 'stdin' while these work: # ( echo "AGTTT" ; echo "ACGTTTTTGGT" ) \ | seqret -sequence=plain::stdin -out=gcg::stdout Reads and writes (returns) sequences !!NA_SEQUENCE 1.0 Length: 16 Type: N Check: 665 .. 1 AGTTTACGTT TTTGGT bash-2.03# ( echo ">FOO" ; echo "ACGTTTTTGGT" ) \ | seqret -sequence=stdin -out=gcg::stdout Reads and writes (returns) sequences !!NA_SEQUENCE 1.0 FOO Length: 11 Type: N Check: 5205 .. 1 ACGTTTTTGG T According the seqret blurb the program is supposed to try one format at a time until it finds something that works. In the first case it seems not to be trying "plain". This was for use with a CGI script, where it's hard to control what the user enters into the box/uploads. EMBOSS-2.2.0 on Solaris 5.8. ( 2.3.1 is current but I'm waiting for 2.4 before upgrading). Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From spjamjai at yahoo.com Sat May 11 06:44:30 2002 From: spjamjai at yahoo.com (=?iso-8859-1?q?Jai=20Shankar?=) Date: Sat, 11 May 2002 11:44:30 +0100 (BST) Subject: No subject Message-ID: <20020511104430.79532.qmail@web20503.mail.yahoo.com> Sir, Can you help me how to retrive the source code of EMBOSS. I downloaded EMBOSS-2.3.1 file from the net. In this I can't get the source code of EMBOSS. So help me how to get the source code of EMBOSS in detail. yours sincerely, S.P.Jaishankar __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From spjamjai at yahoo.com Sat May 11 10:09:49 2002 From: spjamjai at yahoo.com (=?iso-8859-1?q?Jai=20Shankar?=) Date: Sat, 11 May 2002 15:09:49 +0100 (BST) Subject: help regarding Rebaseextract Message-ID: <20020511140949.5221.qmail@web20504.mail.yahoo.com> hai, Can you help me how to run REBASEEXTRACT module. I downloaded emboss in red hat linux system. When I am working with modules remap,restrict , I am getting error as follows : " EMBOSS An error in restrict.c at line 141; cannot locate enzyme file. Run REBASEEXTRACT " Then I run rebaseextract , but it asking " Full pathname of WITHREFM : ",So i can't run rebaseextract. So help me in detail how to run rebaseextract and how to answer for the command " Full pathname of WITHREFM :". Thanks in advance. __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From spjamjai at yahoo.com Sun May 12 05:41:04 2002 From: spjamjai at yahoo.com (=?iso-8859-1?q?Jai=20Shankar?=) Date: Sun, 12 May 2002 10:41:04 +0100 (BST) Subject: help regarding Rebaseextract In-Reply-To: <200205111445.PAA19032@bromine.hgmp.mrc.ac.uk> Message-ID: <20020512094104.87321.qmail@web20504.mail.yahoo.com> HAI, Thank you for your kind help. Yes, I have downloaded files embossre.enz,embossre.sup,embossre.ref in my system. But still I am unable to run REBASEEXTRACT , its giving an error as follows : " EMBOSS An error in rebaseextract.c at line 125: Invalid withrefm file " So help me how to clear this problem and to run rebaseextract. thanking you. --- ableasby at hgmp.mrc.ac.uk wrote: > Go to ftp://ftp.neb.com/pub/rebase/ and you'll find > a withrefm file > there (withrefm.205 currently). > > HTH > > Alan Bleasby > HGMP > __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From ableasby at hgmp.mrc.ac.uk Sun May 12 15:18:07 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sun, 12 May 2002 20:18:07 +0100 (BST) Subject: EMBOSS 2.4.0 available Message-ID: <200205121918.UAA08802@bromine.hgmp.mrc.ac.uk> EMBOSS 2.4.0 has so many changes over 2.3.1 that it is inappropriate to list all of them here. Instead, see the ChangeLog file in the distribution. It is available from http://www.uk.embnet.org/Software/EMBOSS Some Highlights are: Sequence version number (etc) handling New indexing Ability to access SRS servers through a web proxy New programs (Yank, Union, Tranalign) New Jemboss authorising server (including installation scripts) Instructions for site managers wishing to set up a Jemboss authorising server can be found under http://www.uk.embnet.org/Software/EMBOSS/Jemboss Alan 12th May 2002 From GUIDO.STEINER at Roche.COM Mon May 13 03:15:41 2002 From: GUIDO.STEINER at Roche.COM (Steiner, Guido {PRBI~Basel}) Date: Mon, 13 May 2002 09:15:41 +0200 Subject: Emboss 2.4.0: Tar file corrupt? Message-ID: Hi, just downloaded the archive twice, but: tar: directory checksum error Same problem anyone? :) Regards, Guido Steiner -- Guido Steiner, PhD F. Hoffmann-La Roche AG PRBI-B Bioinformatics Building 65/308 CH-3070 Basel Tel. +41 61 6883329 From GUIDO.STEINER at Roche.COM Mon May 13 03:41:36 2002 From: GUIDO.STEINER at Roche.COM (Steiner, Guido {PRBI~Basel}) Date: Mon, 13 May 2002 09:41:36 +0200 Subject: Oops Message-ID: Please ignore my preceding posting. Sorry. Alan Bleasby wrote: > Silly question but I have to ask... you did gunzip it > first I hope? Well, I always try to avoid that since it makes the file even bigger. :) Args, what can I say. It's monday morning at least... > It works as far away as Thailand I know for a fact :-) In Switzerland it now works, too, to provide some feedback. :) Thanks, Alan. :) Guido -- Guido Steiner, PhD F. Hoffmann-La Roche AG PRBI-B Bioinformatics Building 65/308 CH-3070 Basel Tel. +41 61 6883329 From peter.rice at uk.lionbioscience.com Mon May 13 06:20:17 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Mon, 13 May 2002 11:20:17 +0100 Subject: seqret reading from stdin with unkown type References: Message-ID: <3CDF9361.FA3BFAAF@uk.lionbioscience.com> David Mathog wrote: > > I don't understand why this one fails: > > # ( echo "AGTTT" ; echo "ACGTTTTTGGT" ) \ > | seqret -sequence=stdin -out=gcg::stdout > Reads and writes (returns) sequences > Error: Unable to read sequence 'stdin' > > According the seqret blurb the program is supposed to try > one format at a time until it finds something that works. In > the first case it seems not to be trying "plain". Works for me (with 2.4.0). Plain is not used by default, but "raw" is, which should accept alphanumeric characters and 'whitespace', defined as ajRegCompC("[^A-Za-z0-9 \t\n\r]") but reject anything else. The trouble with "plain" (also called "text") is that it can accept anything, usually with the wrong results. It silently removes non-sequence characters from any input. As a default format, this a "A Bad Thing." Turning it off lets us generate the error messages for bad formats. So, the real questions is "why does your script fail with -sf raw" ? One possibility is a problem with some of the other default formats not cleaning up properly, which was fixed in 2.3.0. Can you try with "seqret -debug -sf raw" and send the seqret.dbg file, just to check. I think all you need to do is upgrade to 2.4.0 and all should be well. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From pgalante at compbio.ludwig.org.br Mon May 13 11:39:56 2002 From: pgalante at compbio.ludwig.org.br (Pedro A. F. Galante) Date: Mon, 13 May 2002 12:39:56 -0300 (BRT) Subject: I have a little problem. Message-ID: Hello, I'm having problem with EMBOSS program tfscan. I downloaded the TRANSFAC database and did every steps to intall. The tfscan is working without error, however it don't find any transcription factor, same with sequences that have. Somebory known what is the problem? From mathog at mendel.bio.caltech.edu Tue May 14 12:22:59 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Tue, 14 May 2002 09:22:59 -0700 Subject: ESIM4, was: Re: EMBOSS 2.4.0 available Message-ID: > EMBOSS 2.4.0 has so many changes over 2.3.1 ... esim4, the EMBASSY variant of sim4 (compare mRNA to genomic dna quickly and find alignments) is (still) available from: ftp://saf.bio.caltech.edu/pub/software/molbio/ESIM4-1.0.2.tar.gz This built ok on Solaris but Alan tells me it has problems on AIX which is why it hasn't made it into the main EMBASSY distribution site yet. Those of you not on AIX might want to install it anyway since it's very much faster than est2genome. Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From ableasby at hgmp.mrc.ac.uk Tue May 14 17:51:09 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 14 May 2002 22:51:09 +0100 (BST) Subject: EMBOSS 2.4.1 released Message-ID: <200205142151.WAA10402@bromine.hgmp.mrc.ac.uk> EMBOSS 2.4.1 is a bugfix release. It fixes three issues. a) Programs which tried retrieving sequences from more than one indexed database within the same query could crash. This bug, introduced in 2.4.0, was deemed adequate grounds for this release. b) Indexing of REFSEQ failed. Underscores had been disallowed in IDs from GenBank format entries. c) Improperly terminated sequence files were not readable by MacOSX As usual, more QA tests have been added in the light of the above. These tests (over 600) are performed before each release. Alan From Kohji-OKAMURA at UMIN.ac.jp Wed May 15 05:22:09 2002 From: Kohji-OKAMURA at UMIN.ac.jp (Kohji OKAMURA) Date: Wed, 15 May 2002 18:22:09 +0900 Subject: About Compiling Message-ID: <3CE228C1.1D05A68C@UMIN.ac.jp> Dear Sirs/Mesdames, Hello. I am very grateful for your useful progams at EMBOSS. I'm verry sorry to bother you, but I have some questions about compiling these programs. I could successfully comile "cpgplot" and "eprimer3", but they showed me error messages like below. ld.so.1: ./cpgplot: fatal: libX11.so.6.1: open failed: No such file or directory ld.so.1: ./eprimer3: fatal: libX11.so.6.1: open failed: No such file or directory I'd be happy if you could give me some advice. Thank you for your cooperation. I'm looking forward to having your reply. Good luck with your work! Bye! Sincerely yours, Kohji OKAMURA From ableasby at hgmp.mrc.ac.uk Wed May 15 17:15:08 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 15 May 2002 22:15:08 +0100 (BST) Subject: ESIM4 embassy package Message-ID: <200205152115.WAA26298@bromine.hgmp.mrc.ac.uk> ESIM4 is now available on the EMBOSS ftp server as an EMBASSY (associated) package (ftp://ftp.uk.embnet.org/pub/EMBOSS/) It is also provided on the CVS server. The port was by David Mathog. Alan From sgmd at genetik.fu-berlin.de Fri May 17 07:57:56 2002 From: sgmd at genetik.fu-berlin.de (Thomas Siegmund) Date: Fri, 17 May 2002 13:57:56 +0200 Subject: EMBOSS.kaptn - X11/KDE GUI for EMBOSS 2.4 Message-ID: <200205171357.56451.sgmd@genetik.fu-berlin.de> Dear EMBOSS users, the latest version of the Kaptain user interface for EMBOSS is ready for download. EMBOSS.kaptn 0.78 supports all applications of EMBOSS 2.4.1 and some of the embossified Phylip 3.5. As usual, you will find a compressed tar archive for download, additional information, and a few screenshots at http://userpage.fu-berlin.de/~sgmd . From the ChangeLog: Version 0.78 - Finished support for EMBOSS 2.4 - report output for marscan.kaptn, patmatdb.kaptn, patmatmotifs.kaptn equicktandem.kaptn, etandem.kaptn - removed staden option from dbi*.kaptn - renamed -filename to -filenames in dbiblast.kaptn - fix for fuzztran.kaptn, fuzznuc.kaptn, fuzzpro.kaptn - new: yank.kaptn, union.kaptn Version 0.77 - new: tranalign.kaptn - fields and maxindex qualifiers for dbiblast.kaptn, dbifasta.kaptn, dbigcg.kaptn, dbiflat.kaptn - exclude qualifier for dbiblast.kaptn, dbigcg.kaptn - report output for fuzztran.kaptn, fuzznuc.kaptn, fuzzpro.kaptn Version 0.76 -new: eprotdist.kaptn, ednadist.kaptn, egendist.kaptn, eseqboot.kaptn efactor.kaptn, edollop.kaptn, ednainvar.kaptn Version 0.75 - better design for eneighbor.kaptn, ekitsch.kaptn - new: efitch.kaptn, epenny.kaptn, edolpenny.kaptn Version 0.74 - small fix in merger.kaptn & megamerger.kaptn, replace "-stout" by "-outfile stdout" - new: eneighbor.kaptn Version 0.73 - starting ephylip - new: ednapars.kaptn, ednapenny.kaptn, emix.kaptn eprotpars.kaptn, erestml.kaptn, ekitsch.kaptn Please let me know if I missed something in EMBOSS 2.4, that changelog was a bit longer than usual. Have a nice weekend Thomas -- Thomas Siegmund Freie Universit?t Berlin Institut f?r Genetik Arnimallee 7 14195 Berlin Germany Tel: +49 30 838 54868 Fax: +49 30 838 54395 http://userpage.fu-berlin.de/~sgmd From daniel at mrc-lmb.cam.ac.uk Fri May 17 09:03:11 2002 From: daniel at mrc-lmb.cam.ac.uk (Daniel Schlieper) Date: Fri, 17 May 2002 14:03:11 +0100 (BST) Subject: seqed? Message-ID: Hello, I really like emboss, and I use it as much as I can. In fact, the only reason to start a GCG session is seqed. I couldn't find anything like it in emboss. tfm newseq writes: "You wouldn't want to type a long sequence in by hand, anyway, would you?" Maybe I am old fashioned, but yes, I do. As I can type quickly, 1000 nt are not a problem, and sometimes the only way to get the sequence file. But this can only be done with a program that not only allows to type in nucleotides, but also to check them, to look for given sequences and so on. It will be even more helpfulll if it ignores blanks, carriage returns and numbers (for cut-and-paste). So I would be glad if you please add a seqed clone to the emboss suite. Best regards, Daniel -- Daniel Schlieper MRC Laboratory of Molecular Biology daniel at mrc-lmb.cam.ac.uk Hills Road, Cambridge CB2 2QH, UK Tel.: +44 1223 252969 FAX: +44 1223 213556 WWW: http://www2.mrc-lmb.cam.ac.uk/groups/JYL/index.html From gwilliam at hgmp.mrc.ac.uk Fri May 17 09:06:43 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Fri, 17 May 2002 14:06:43 +0100 Subject: seqed? References: Message-ID: <3CE50063.4459056@hgmp.mrc.ac.uk> Try 'mse http://www.uk.embnet.org/Software/EMBOSS/EMBASSY/MSE/mse.html This is an EMBASSY program, so has to be set up separately to the main EMBOSS distribution, which is why you may not have seen it. Gary Daniel Schlieper wrote: > > Hello, > > I really like emboss, and I use it as much as I can. In fact, the only > reason to start a GCG session is seqed. I couldn't find anything like it > in emboss. tfm newseq writes: "You wouldn't want to type a long sequence > in by hand, anyway, would you?" Maybe I am old fashioned, but yes, I do. > As I can type quickly, 1000 nt are not a problem, and sometimes the only > way to get the sequence file. > > But this can only be done with a program that not only allows to type in > nucleotides, but also to check them, to look for given sequences > and so on. It will be even more helpfulll if it ignores blanks, carriage > returns and numbers (for cut-and-paste). > > So I would be glad if you please add a seqed clone to the emboss suite. > > Best regards, Daniel > > -- > Daniel Schlieper MRC Laboratory of Molecular Biology > daniel at mrc-lmb.cam.ac.uk Hills Road, Cambridge CB2 2QH, UK > Tel.: +44 1223 252969 FAX: +44 1223 213556 > WWW: http://www2.mrc-lmb.cam.ac.uk/groups/JYL/index.html -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From daniel at mrc-lmb.cam.ac.uk Fri May 17 09:36:21 2002 From: daniel at mrc-lmb.cam.ac.uk (Daniel Schlieper) Date: Fri, 17 May 2002 14:36:21 +0100 (BST) Subject: seqed? In-Reply-To: <3CE50063.4459056@hgmp.mrc.ac.uk> Message-ID: Dear Gary, thank you very much. Yes mse is a bit hidden, but Peter Rice was as kind as to point me to that. In total, mse seems to be much better than seqed, and I will be happy to use it. Just in case if there is anybody interested in even improving it, there might two minor improvments possible: 1. There could be a check feature as in seqed. For example (from seqed): aacgggttaaggcct ^ ^^^^ aaccggttaaccggt ....|.........|.........|.... 0 10 20 2. There could be a way to read an empty (or not yet existing file). Now it says: Unix % mse i.seq Multiple Sequence Editor Error: failed to open filename i.seq Error: Unable to read sequence 'i.seq' Many thanks and best regards, Daniel -- Daniel Schlieper MRC Laboratory of Molecular Biology daniel at mrc-lmb.cam.ac.uk Hills Road, Cambridge CB2 2QH, UK Tel.: +44 1223 252969 FAX: +44 1223 213556 WWW: http://www2.mrc-lmb.cam.ac.uk/groups/JYL/index.html On Fri, 17 May 2002, Gary Williams, Tel 01223 494522 wrote: > > Try 'mse > http://www.uk.embnet.org/Software/EMBOSS/EMBASSY/MSE/mse.html > > This is an EMBASSY program, so has to be set up separately to the main > EMBOSS distribution, which is why you may not have seen it. > > Gary > > Daniel Schlieper wrote: > > > > Hello, > > > > I really like emboss, and I use it as much as I can. In fact, the only > > reason to start a GCG session is seqed. I couldn't find anything like it > > in emboss. tfm newseq writes: "You wouldn't want to type a long sequence > > in by hand, anyway, would you?" Maybe I am old fashioned, but yes, I do. > > As I can type quickly, 1000 nt are not a problem, and sometimes the only > > way to get the sequence file. > > > > But this can only be done with a program that not only allows to type in > > nucleotides, but also to check them, to look for given sequences > > and so on. It will be even more helpfulll if it ignores blanks, carriage > > returns and numbers (for cut-and-paste). > > > > So I would be glad if you please add a seqed clone to the emboss suite. > > > > Best regards, Daniel > > > > -- > > Daniel Schlieper MRC Laboratory of Molecular Biology > > daniel at mrc-lmb.cam.ac.uk Hills Road, Cambridge CB2 2QH, UK > > Tel.: +44 1223 252969 FAX: +44 1223 213556 > > WWW: http://www2.mrc-lmb.cam.ac.uk/groups/JYL/index.html > > -- > Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 > mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ > Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK > > From peter.rice at uk.lionbioscience.com Fri May 17 09:57:02 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 17 May 2002 14:57:02 +0100 Subject: seqed? References: Message-ID: <3CE50C2E.2C1D0ACF@uk.lionbioscience.com> Daniel Schlieper wrote: > > thank you very much. Yes mse is a bit hidden, but Peter Rice was as kind > as to point me to that. In total, mse seems to be much better than seqed, > and I will be happy to use it. > > Just in case if there is anybody interested in even improving it, there > might two minor improvments possible: > > 1. There could be a check feature as in seqed. For example (from seqed): > > aacgggttaaggcct > ^ ^^^^ > aaccggttaaccggt > ....|.........|.........|.... > 0 10 20 Aaaahhhhh .... that is rather nasty to implement. In SEQED it was really there for people typing in data from sequencing gels, and in particular for the "digitizer" input (a digitizer was a table with a pen where you clicked the pen tip on the 4 corners, on the lanes, and then on each band). The check mode was to compare two runs in order to catch clicks that were in between bands. Far simpler is to simply enter the sequence twice, then use wordmatch to compare them (again, that is basically what I used to do with SEQED anyway). > 2. There could be a way to read an empty (or not yet existing file). Now > it says: > > Unix % mse i.seq > Multiple Sequence Editor > Error: failed to open filename i.seq > Error: Unable to read sequence 'i.seq' That one is a simple EMBOSS global change, allowing an input "sequence set" to be empty. Basically, adding the nullok attribute for sequences, or perhaps a minimum number of sequences for a sequence set (default 1, emma would like more, mse could handle 0). Expect something in a future release. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From tmargus at ebc.ee Mon May 20 12:00:15 2002 From: tmargus at ebc.ee (=?iso-8859-1?Q?T=F5nu_Margus?=) Date: Mon, 20 May 2002 19:00:15 +0300 Subject: installing EMBOSS 2.4.1 and EMBASSY Message-ID: <00d701c20017$c1c47240$1e1728c1@ebc.ee> Hi, First problem installing EMBOSS ( op-sys LINUX slackware 8.0) ./configure runs ok but make gives an error % make .......... gcc -g -O2 -o .libs/abiview abiview.o ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so ../ajax/.libs/libajax.so ../plplot/.libs/libplplot.so -L/usr/X11R6/lib -lX11 -lm -Wl,--rpath -Wl,/usr/local/bin1/emboss/lib ../plplot/.libs/libplplot.so: undefined reference to `atexit' collect2: ld returned 1 exit status make[2]: *** [abiview] Error 1 in some reason it didn't find atexit so I comment it out from plplot/tek.c /*#ifdef STDC_HEADERS if (atexit(tty_atexit)) (void) fprintf(stderr, "Unable to set up atexit handler.\n"); #endif*/ return; Now it compiles without problems Second problem arouse when I tried to install MEME ./configure didn't find the file ./../../ltconfig cd /programs/EMBOSS-2.4.1/embassy/MEME-2.3.1/ ./configure --prefix=/usr/local/bin1/emboss updating cache ./config.cache ./../../ltconfig: ./../../ltconfig: No such file or directory configure: error: libtool configure failed Same problems appears with MSE-0.0.4 PHYLIP and HMMER installed without problems. Sincerely yours Tonu Margus Estonian Biocenter & Tartu University Riia 23 Tartu 51010 Estonia E-mail tmargus at ebc.ee -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20020520/15b9ad5b/attachment.html From ekolomiets at yahoo.com Wed May 22 13:13:59 2002 From: ekolomiets at yahoo.com (Elena Kolomiets) Date: Wed, 22 May 2002 10:13:59 -0700 (PDT) Subject: Database set up Q's Message-ID: <20020522171359.43290.qmail@web13805.mail.yahoo.com> Hello, i am looking for detaile description of whow to set up my oun Database definition. How .embossrc and .embossdata works along with emboss.default? My showdb result in listing test databases even though the emboss_tempdata variable commented in emboss.default file???!!! ===== Sincerely, Elena Kolomiets 3927 Hawk Owl Cove, College Station, TX 77845 (979)690-3172 __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From ekolomiets at yahoo.com Wed May 22 13:44:52 2002 From: ekolomiets at yahoo.com (Elena Kolomiets) Date: Wed, 22 May 2002 10:44:52 -0700 (PDT) Subject: Database set up Q's Message-ID: <20020522174452.50118.qmail@web13805.mail.yahoo.com> Hello, i am looking for detaile description of whow to set up my oun Database definition. How .embossrc and .embossdata works along with emboss.default? My showdb result in listing test databases even though the emboss_tempdata variable commented in emboss.default file???!!! ===== Sincerely, Elena Kolomiets 3927 Hawk Owl Cove, College Station, TX 77845 (979)690-3172 __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From David.Bauer at SCHERING.DE Thu May 23 01:48:58 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Thu, 23 May 2002 07:48:58 +0200 Subject: Antwort: Database set up Q's Message-ID: Hi, there is a very usefull adminguide written by David Martin at http://www.uk.embnet.org/Software/EMBOSS/admin.html It contains a detailed description of setting up databases to work with emboss. David. Hello, i am looking for detaile description of whow to set up my oun Database definition. How .embossrc and .embossdata works along with emboss.default? My showdb result in listing test databases even though the emboss_tempdata variable commented in emboss.default file???!!! ===== Sincerely, Elena Kolomiets 3927 Hawk Owl Cove, College Station, TX 77845 (979)690-3172 __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From gwilliam at hgmp.mrc.ac.uk Thu May 23 04:18:26 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 23 May 2002 09:18:26 +0100 Subject: Antwort: Database set up Q's References: Message-ID: <3CECA5D2.D4DA1166@hgmp.mrc.ac.uk> See also the description of the database specification syntax at: http://www.uk.embnet.org/Software/EMBOSS/Usa/databases.html Gary David.Bauer at SCHERING.DE wrote: > > Hi, > > there is a very usefull adminguide written by David Martin at > > http://www.uk.embnet.org/Software/EMBOSS/admin.html > > It contains a detailed description of setting up databases to work with emboss. > > David. > > Hello, > i am looking for detaile description of whow to set up > > my oun Database definition. > How .embossrc and .embossdata works along with > emboss.default? > My showdb result in listing test databases even though > the emboss_tempdata variable commented in > emboss.default file???!!! > > ===== > Sincerely, > > Elena Kolomiets > 3927 Hawk Owl Cove, > College Station, TX 77845 > (979)690-3172 > > __________________________________________________ > Do You Yahoo!? > LAUNCH - Your Yahoo! Music Experience > http://launch.yahoo.com -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From peter.rice at uk.lionbioscience.com Thu May 23 04:22:24 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 23 May 2002 09:22:24 +0100 Subject: Database set up Q's References: <20020522171359.43290.qmail@web13805.mail.yahoo.com> Message-ID: <3CECA6C0.EC5FC4DF@uk.lionbioscience.com> Elena Kolomiets wrote: > > i am looking for detaile description of whow to set up > > my oun Database definition. > How .embossrc and .embossdata works along with > emboss.default? > My showdb result in listing test databases even though > the emboss_tempdata variable commented in > emboss.default file???!!! You need to comment out the DB lines for the test databases to remove them. Commenting out emboss_tempdata means the test databases are still defined, but will not work. I am working on adding more comments to emboss.default.template and updating the Admin Guide and web pages. Of course, updating emboss.default.template may not help users who already have their own emboss.default file so we can make comments in the next release notes too to make sure they see the updates. regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From dmamartin at dundee.ac.uk Thu May 23 04:28:49 2002 From: dmamartin at dundee.ac.uk (David Martin) Date: Thu, 23 May 2002 09:28:49 +0100 (BST) Subject: Antwort: Database set up Q's In-Reply-To: <3CECA5D2.D4DA1166@hgmp.mrc.ac.uk> Message-ID: On Thu, 23 May 2002, Gary Williams, Tel 01223 494522 wrote: > > See also the description of the database specification syntax at: > http://www.uk.embnet.org/Software/EMBOSS/Usa/databases.html > There have been a number of changes in EMBOSS that add more functionality to the database definitions since the admin guide was last updated by me. Everything in the admin guide is more or less valid (some of the platform specific stuff is a bit dated, ie OS X and IRIX may not be entirely correct now) but misses some of the new bits. Peter Rice has picked up the poisoned chalice of updating the admin guide (probably so I don't fill his email inbox with stupid questions again) and it will be released under a free documentation license in due course. The existing version will get you going for now and is 99% compatible with todays EMBOSS but only covers 75% of the features. ..d ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee +44 1382 348704 9f:2e:d8:b6:fb:fd:2c:77:02:50:ea:c0:d6:af:04:ed ---------------------------------- From peter.rice at uk.lionbioscience.com Thu May 23 04:45:38 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 23 May 2002 09:45:38 +0100 Subject: Database set up Q's References: Message-ID: <3CECAC32.1719C672@uk.lionbioscience.com> David Martin wrote: > > Peter Rice has picked up the poisoned chalice of updating the admin guide > (probably so I don't fill his email inbox with stupid questions again) and > it will be released under a free documentation license in due course. > > The existing version will get you going for now and is 99% compatible with > todays EMBOSS but only covers 75% of the features. So, the obvious request .... please send me all your stupid questions that the Admin Guide should be able to answer. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From p.lopriore at it.ibm.com Fri May 24 12:07:54 2002 From: p.lopriore at it.ibm.com (Pietro Lopriore) Date: Fri, 24 May 2002 18:07:54 +0200 Subject: No subject Message-ID: Hi everybody, a short question: is there a method (a command-line option) so that EMBOSS doesn't write any output result file? I would like to obtain my results in the stdoutput without writing on the file system. Thanks in advance Best regards Pietro _________________________________________________ Pietro Lopriore IBM Java Technology Center via Tridente 42/14 - 70125 BARI - ITALY Tel. +39 .80.5466715 - Fax. +39.80.5466621 Tie Line: 37715 email: p.lopriore at it.ibm.com Web Site: http://www.ibm.com/it/semeasud From peter.rice at uk.lionbioscience.com Fri May 24 12:06:58 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 24 May 2002 17:06:58 +0100 Subject: stdout output References: Message-ID: <3CEE6522.BDE96F72@uk.lionbioscience.com> Pietro Lopriore wrote: > > Hi everybody, > a short question: > is there a method (a command-line option) so that EMBOSS doesn't write any > output result file? > I would like to obtain my results in the stdoutput without writing on the > file system. -stdout will default to standard output for all applications -filter will default to standard input and standard output for all applications (and also, because standard input is in use, defaults to -auto) Some folk (Alan for example) like to define these globally, for example: setenv EMBOSS_STDOUT Y You can put this in your login, or in your .embossrc file This applies only to the first output file. Any secondary output goes to a file. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From simon.andrews at bbsrc.ac.uk Tue May 28 04:40:46 2002 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Tue, 28 May 2002 09:40:46 +0100 Subject: Bug in seqret in EMBOSS 2.4.1 ? Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E2859C@bi-exsrv1.iapc.bbsrc.ac.uk> I think I've found a problem with seqret in v2.4.1. It's failing to fetch sequences from EBIs SRS system, which fetch fine when I use seqret from v2.2.0. My setup in emboss.default is this: DB embl [ type: N method: url format: embl url: "http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[EMBLRELEASE-ACC:%s]" comment: "EBI EMBL ACs" ] Using this under 2.4.1 produces: $ seqret embl:z83307 Reads and writes (returns) sequences Error: Unable to read sequence 'embl:z83307' $ ...and the same thing under 2.2.0 gives: $ seqret embl:z83307 Reads and writes (returns) sequences Output sequence [hsa1280.fasta]: $ Running the latest seqret with -debug shows that the sequence is fetched (you can see it being parsed), but that it is the format recognition at the end which fails. The last bits of the debug file are at the bottom of this message. Is this a bug in seqret, or do I need to update the format of my emboss.default file? Thanks for any help Simon. ################################## :[1] agatgaaaaa ggggagaacc atattatttt ggtcaaaata ttgtggtcca caagcatatg 21960 :[1] ctccagttag tttctttctt gaataaaggc tttttattgt catgtaaaca caagctgtgt 22020 :[1] gcacatgatc aaaatatttt aaaactaaaa ataatttatg aaaaaatatt cttccttgat 22080 :[1] ttcaacctgc ctgtacttat ttttaataca aatatatcta ggataaaaga tactattata 22140 :[1] caaatgcatg atcaaggaag atgtcagaaa ggttaacggg gtcaagaaaa gctgtaacac 22200 :[1] tcatagagta atatccatac agaactattc cttagtatcc atgggaccca gcc 22253 :[1] // removing '' [1] leaving ''' ' [1] [1] :[1] 0 [1] seqRead: seqin format 3 'embl' ajFeattableDel 0 ajFileBuffNoBuff buffsize: 492 ++seqRead known format 3 ++seqReadFmt format 3 (embl) 'embl:z83307' feat No seqReadEmbl first line '620 ' Format 3 (embl) failed, file buffer reset by seqReadFmt ++seqReadFmt failed - nothing read seqRead: (b2) seqReadFmt stat == FAIL *failed* ajFeattableDel 0 seqRead failed - try again with format 3 'embl' ++seqReadFmt format 3 (embl) 'embl:z83307' feat No seqReadEmbl first line '620 ' Format 3 (embl) failed, file buffer reset by seqReadFmt ++seqReadFmt failed - nothing read seqRead: (b3) seqReadFmt stat == FAIL *failed* Failure for option 'sequence' From peter.rice at uk.lionbioscience.com Tue May 28 06:21:35 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 28 May 2002 11:21:35 +0100 Subject: Bug in seqret in EMBOSS 2.4.1 ? References: <2DC41140A89ED411989D00508BDCD9ED01E2859C@bi-exsrv1.iapc.bbsrc.ac.uk> Message-ID: <3CF35A2F.53761480@uk.lionbioscience.com> Hi Simon, > I think I've found a problem with seqret in v2.4.1. It's failing to fetch > sequences from EBIs SRS system, which fetch fine when I use seqret from > v2.2.0. Tricky one ... your definition works fine for me. Can you send the full seqret.dbg file from 2.4.1 and from 2.2.0 regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From krishna at mrna.tn.nic.in Tue May 28 06:32:05 2002 From: krishna at mrna.tn.nic.in (Krishnaswamy S) Date: Tue, 28 May 2002 16:02:05 +0530 (IST) Subject: patmatdb Message-ID: we wish to modify the patmatdb program be modified to search for say 70% similarity to the prosite pattern. How can this be done? Is there a c program source of the prosite scan program available? regards krishnaswamy -- S.Krishnaswamy School of Biotechnology Madurai Kamaraj University Madurai 625 021, India mkubic9 at giasmd01.vsnl.net.in krishna at mrna.tn.nic.in From krishna at mrna.tn.nic.in Tue May 28 06:33:47 2002 From: krishna at mrna.tn.nic.in (Krishnaswamy S) Date: Tue, 28 May 2002 16:03:47 +0530 (IST) Subject: patmatdb - without typos Message-ID: we wish to modify the patmatdb program to search for say 70% similarity to the prosite pattern. How can this be done? Is there a c program source of the prosite scan program available? regards krishnaswamy -- S.Krishnaswamy School of Biotechnology Madurai Kamaraj University Madurai 625 021, India mkubic9 at giasmd01.vsnl.net.in krishna at mrna.tn.nic.in From lukem at gene.pbi.nrc.ca Fri May 3 00:44:36 2002 From: lukem at gene.pbi.nrc.ca (Luke McCarthy) Date: Thu, 2 May 2002 18:44:36 -0600 (CST) Subject: EMBOSS::GUI 1.0 Message-ID: Hi everybody, Last July I announced on this list the development of a Perl CGI graphical interface to the EMBOSS scripts and solicited beta testers. Development has been intermittent since then, but I believe the interface is now ready for public consumption. The GUI scripts generate the application pages dynamically from the EMBOSS ACD files, so it should adapt to newer EMBOSS releases without much hassle (all of the current features that I am aware of are available, including output formats for sequences, features, reports and alignments...) The main menu is generated dynamically as well, so only those tools which are available on your system will be listed (for example, if you haven't installed the EMBASSY stuff it won't show up...) The GUI can be downloaded from http://bioinfo.pbi.nrc.ca/~lukem/EMBOSS or http://www.cbr.nrc.ca/EMBOSS and a demo version is available online at http://bioinfo.pbi.nrc.ca/cgi-bin/emboss-redirect.pl Cheers, Luke McCarthy lukem at bioinfo.pbi.nrc.ca From aiyar at ebv.mimnet.northwestern.edu Fri May 3 01:50:57 2002 From: aiyar at ebv.mimnet.northwestern.edu (Ashok Aiyar) Date: Thu, 2 May 2002 20:50:57 -0500 (CDT) Subject: EMBOSS::GUI 1.0 In-Reply-To: Message-ID: On Thu, 2 May 2002, Luke McCarthy wrote: > Hi everybody, > > Last July I announced on this list the development of a Perl CGI graphical > interface to the EMBOSS scripts and solicited beta testers. Development > has been intermittent since then, but I believe the interface is now ready > for public consumption. > > The GUI can be downloaded from http://bioinfo.pbi.nrc.ca/~lukem/EMBOSS or > http://www.cbr.nrc.ca/EMBOSS and a demo version is available online at > http://bioinfo.pbi.nrc.ca/cgi-bin/emboss-redirect.pl > Can I add that my lab has been using Luke's EMBOSS-GUI for close to a year. It is really simple to install, and does provide a consistent and intuitive user-interface. Thanks Luke! Ashok -- Ashok Aiyar, Ph.D. Assistant Professor email: a-aiyar at northwestern.edu Department of Microbiology-Immunology office: (312) 503-2524 303 E. Chicago Avenue, WARD 4-123 lab: (312) 503-2542 Northwestern University, Chicago, IL 60611 fax: (312) 503-1339 From asen.nenov at metalife.de Tue May 7 13:44:08 2002 From: asen.nenov at metalife.de (Asen Nenov) Date: Tue, 07 May 2002 13:44:08 GMT Subject: unable to open font file?? Message-ID: <20020507.13440800@senski.bg> Hi to All, My EMBOSS(current version) is running on Mandrake 8.1/Duron/256. I tried all of PLOT programs, but all of the are giving me the following message: Cannot open library file: plstnd5.fnt Please set PLPLOT_LIB to the plplot/lib directory under emboss *** PLPLOT ERROR *** Unable to open font file Can anyone help me eith this issue? Any help appreciated. Best Regards Asen From dmamartin at dundee.ac.uk Tue May 7 15:39:09 2002 From: dmamartin at dundee.ac.uk (David Martin) Date: Tue, 7 May 2002 16:39:09 +0100 (BST) Subject: unable to open font file?? In-Reply-To: <20020507.13440800@senski.bg> Message-ID: On Tue, 7 May 2002, Asen Nenov wrote: > Hi to All, > > My EMBOSS(current version) is running on Mandrake 8.1/Duron/256. > I tried all of PLOT programs, but all of the are giving me the following > message: > > Cannot open library file: plstnd5.fnt > Please set PLPLOT_LIB to the plplot/lib directory under emboss > > *** PLPLOT ERROR *** > > Unable to open font file > > Can anyone help me eith this issue? > Any help appreciated. The error is somewhat misleading and is correct only if you are running from the source directory. If you have installed (with 'make install') then copy the font files plstnd5.fnt and plxtnd5.fnt to the share/EMBOSS directory (typically /usr/local/share/EMBOSS unless you have configured with --prefix=/somewhere ) You will find these files in /plplot/lib Hope this helps ..d > > Best Regards > Asen > ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee +44 1382 348704 ---------------------------------- From mathog at mendel.bio.caltech.edu Fri May 10 21:35:45 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Fri, 10 May 2002 14:35:45 -0700 Subject: seqret reading from stdin with unkown type Message-ID: I don't understand why this one fails: # ( echo "AGTTT" ; echo "ACGTTTTTGGT" ) \ | seqret -sequence=stdin -out=gcg::stdout Reads and writes (returns) sequences Error: Unable to read sequence 'stdin' while these work: # ( echo "AGTTT" ; echo "ACGTTTTTGGT" ) \ | seqret -sequence=plain::stdin -out=gcg::stdout Reads and writes (returns) sequences !!NA_SEQUENCE 1.0 Length: 16 Type: N Check: 665 .. 1 AGTTTACGTT TTTGGT bash-2.03# ( echo ">FOO" ; echo "ACGTTTTTGGT" ) \ | seqret -sequence=stdin -out=gcg::stdout Reads and writes (returns) sequences !!NA_SEQUENCE 1.0 FOO Length: 11 Type: N Check: 5205 .. 1 ACGTTTTTGG T According the seqret blurb the program is supposed to try one format at a time until it finds something that works. In the first case it seems not to be trying "plain". This was for use with a CGI script, where it's hard to control what the user enters into the box/uploads. EMBOSS-2.2.0 on Solaris 5.8. ( 2.3.1 is current but I'm waiting for 2.4 before upgrading). Thanks, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From spjamjai at yahoo.com Sat May 11 10:44:30 2002 From: spjamjai at yahoo.com (=?iso-8859-1?q?Jai=20Shankar?=) Date: Sat, 11 May 2002 11:44:30 +0100 (BST) Subject: No subject Message-ID: <20020511104430.79532.qmail@web20503.mail.yahoo.com> Sir, Can you help me how to retrive the source code of EMBOSS. I downloaded EMBOSS-2.3.1 file from the net. In this I can't get the source code of EMBOSS. So help me how to get the source code of EMBOSS in detail. yours sincerely, S.P.Jaishankar __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From spjamjai at yahoo.com Sat May 11 14:09:49 2002 From: spjamjai at yahoo.com (=?iso-8859-1?q?Jai=20Shankar?=) Date: Sat, 11 May 2002 15:09:49 +0100 (BST) Subject: help regarding Rebaseextract Message-ID: <20020511140949.5221.qmail@web20504.mail.yahoo.com> hai, Can you help me how to run REBASEEXTRACT module. I downloaded emboss in red hat linux system. When I am working with modules remap,restrict , I am getting error as follows : " EMBOSS An error in restrict.c at line 141; cannot locate enzyme file. Run REBASEEXTRACT " Then I run rebaseextract , but it asking " Full pathname of WITHREFM : ",So i can't run rebaseextract. So help me in detail how to run rebaseextract and how to answer for the command " Full pathname of WITHREFM :". Thanks in advance. __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From spjamjai at yahoo.com Sun May 12 09:41:04 2002 From: spjamjai at yahoo.com (=?iso-8859-1?q?Jai=20Shankar?=) Date: Sun, 12 May 2002 10:41:04 +0100 (BST) Subject: help regarding Rebaseextract In-Reply-To: <200205111445.PAA19032@bromine.hgmp.mrc.ac.uk> Message-ID: <20020512094104.87321.qmail@web20504.mail.yahoo.com> HAI, Thank you for your kind help. Yes, I have downloaded files embossre.enz,embossre.sup,embossre.ref in my system. But still I am unable to run REBASEEXTRACT , its giving an error as follows : " EMBOSS An error in rebaseextract.c at line 125: Invalid withrefm file " So help me how to clear this problem and to run rebaseextract. thanking you. --- ableasby at hgmp.mrc.ac.uk wrote: > Go to ftp://ftp.neb.com/pub/rebase/ and you'll find > a withrefm file > there (withrefm.205 currently). > > HTH > > Alan Bleasby > HGMP > __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From ableasby at hgmp.mrc.ac.uk Sun May 12 19:18:07 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sun, 12 May 2002 20:18:07 +0100 (BST) Subject: EMBOSS 2.4.0 available Message-ID: <200205121918.UAA08802@bromine.hgmp.mrc.ac.uk> EMBOSS 2.4.0 has so many changes over 2.3.1 that it is inappropriate to list all of them here. Instead, see the ChangeLog file in the distribution. It is available from http://www.uk.embnet.org/Software/EMBOSS Some Highlights are: Sequence version number (etc) handling New indexing Ability to access SRS servers through a web proxy New programs (Yank, Union, Tranalign) New Jemboss authorising server (including installation scripts) Instructions for site managers wishing to set up a Jemboss authorising server can be found under http://www.uk.embnet.org/Software/EMBOSS/Jemboss Alan 12th May 2002 From GUIDO.STEINER at Roche.COM Mon May 13 07:15:41 2002 From: GUIDO.STEINER at Roche.COM (Steiner, Guido {PRBI~Basel}) Date: Mon, 13 May 2002 09:15:41 +0200 Subject: Emboss 2.4.0: Tar file corrupt? Message-ID: Hi, just downloaded the archive twice, but: tar: directory checksum error Same problem anyone? :) Regards, Guido Steiner -- Guido Steiner, PhD F. Hoffmann-La Roche AG PRBI-B Bioinformatics Building 65/308 CH-3070 Basel Tel. +41 61 6883329 From GUIDO.STEINER at Roche.COM Mon May 13 07:41:36 2002 From: GUIDO.STEINER at Roche.COM (Steiner, Guido {PRBI~Basel}) Date: Mon, 13 May 2002 09:41:36 +0200 Subject: Oops Message-ID: Please ignore my preceding posting. Sorry. Alan Bleasby wrote: > Silly question but I have to ask... you did gunzip it > first I hope? Well, I always try to avoid that since it makes the file even bigger. :) Args, what can I say. It's monday morning at least... > It works as far away as Thailand I know for a fact :-) In Switzerland it now works, too, to provide some feedback. :) Thanks, Alan. :) Guido -- Guido Steiner, PhD F. Hoffmann-La Roche AG PRBI-B Bioinformatics Building 65/308 CH-3070 Basel Tel. +41 61 6883329 From peter.rice at uk.lionbioscience.com Mon May 13 10:20:17 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Mon, 13 May 2002 11:20:17 +0100 Subject: seqret reading from stdin with unkown type References: Message-ID: <3CDF9361.FA3BFAAF@uk.lionbioscience.com> David Mathog wrote: > > I don't understand why this one fails: > > # ( echo "AGTTT" ; echo "ACGTTTTTGGT" ) \ > | seqret -sequence=stdin -out=gcg::stdout > Reads and writes (returns) sequences > Error: Unable to read sequence 'stdin' > > According the seqret blurb the program is supposed to try > one format at a time until it finds something that works. In > the first case it seems not to be trying "plain". Works for me (with 2.4.0). Plain is not used by default, but "raw" is, which should accept alphanumeric characters and 'whitespace', defined as ajRegCompC("[^A-Za-z0-9 \t\n\r]") but reject anything else. The trouble with "plain" (also called "text") is that it can accept anything, usually with the wrong results. It silently removes non-sequence characters from any input. As a default format, this a "A Bad Thing." Turning it off lets us generate the error messages for bad formats. So, the real questions is "why does your script fail with -sf raw" ? One possibility is a problem with some of the other default formats not cleaning up properly, which was fixed in 2.3.0. Can you try with "seqret -debug -sf raw" and send the seqret.dbg file, just to check. I think all you need to do is upgrade to 2.4.0 and all should be well. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From pgalante at compbio.ludwig.org.br Mon May 13 15:39:56 2002 From: pgalante at compbio.ludwig.org.br (Pedro A. F. Galante) Date: Mon, 13 May 2002 12:39:56 -0300 (BRT) Subject: I have a little problem. Message-ID: Hello, I'm having problem with EMBOSS program tfscan. I downloaded the TRANSFAC database and did every steps to intall. The tfscan is working without error, however it don't find any transcription factor, same with sequences that have. Somebory known what is the problem? From mathog at mendel.bio.caltech.edu Tue May 14 16:22:59 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Tue, 14 May 2002 09:22:59 -0700 Subject: ESIM4, was: Re: EMBOSS 2.4.0 available Message-ID: > EMBOSS 2.4.0 has so many changes over 2.3.1 ... esim4, the EMBASSY variant of sim4 (compare mRNA to genomic dna quickly and find alignments) is (still) available from: ftp://saf.bio.caltech.edu/pub/software/molbio/ESIM4-1.0.2.tar.gz This built ok on Solaris but Alan tells me it has problems on AIX which is why it hasn't made it into the main EMBASSY distribution site yet. Those of you not on AIX might want to install it anyway since it's very much faster than est2genome. Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From ableasby at hgmp.mrc.ac.uk Tue May 14 21:51:09 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 14 May 2002 22:51:09 +0100 (BST) Subject: EMBOSS 2.4.1 released Message-ID: <200205142151.WAA10402@bromine.hgmp.mrc.ac.uk> EMBOSS 2.4.1 is a bugfix release. It fixes three issues. a) Programs which tried retrieving sequences from more than one indexed database within the same query could crash. This bug, introduced in 2.4.0, was deemed adequate grounds for this release. b) Indexing of REFSEQ failed. Underscores had been disallowed in IDs from GenBank format entries. c) Improperly terminated sequence files were not readable by MacOSX As usual, more QA tests have been added in the light of the above. These tests (over 600) are performed before each release. Alan From Kohji-OKAMURA at UMIN.ac.jp Wed May 15 09:22:09 2002 From: Kohji-OKAMURA at UMIN.ac.jp (Kohji OKAMURA) Date: Wed, 15 May 2002 18:22:09 +0900 Subject: About Compiling Message-ID: <3CE228C1.1D05A68C@UMIN.ac.jp> Dear Sirs/Mesdames, Hello. I am very grateful for your useful progams at EMBOSS. I'm verry sorry to bother you, but I have some questions about compiling these programs. I could successfully comile "cpgplot" and "eprimer3", but they showed me error messages like below. ld.so.1: ./cpgplot: fatal: libX11.so.6.1: open failed: No such file or directory ld.so.1: ./eprimer3: fatal: libX11.so.6.1: open failed: No such file or directory I'd be happy if you could give me some advice. Thank you for your cooperation. I'm looking forward to having your reply. Good luck with your work! Bye! Sincerely yours, Kohji OKAMURA From ableasby at hgmp.mrc.ac.uk Wed May 15 21:15:08 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 15 May 2002 22:15:08 +0100 (BST) Subject: ESIM4 embassy package Message-ID: <200205152115.WAA26298@bromine.hgmp.mrc.ac.uk> ESIM4 is now available on the EMBOSS ftp server as an EMBASSY (associated) package (ftp://ftp.uk.embnet.org/pub/EMBOSS/) It is also provided on the CVS server. The port was by David Mathog. Alan From sgmd at genetik.fu-berlin.de Fri May 17 11:57:56 2002 From: sgmd at genetik.fu-berlin.de (Thomas Siegmund) Date: Fri, 17 May 2002 13:57:56 +0200 Subject: EMBOSS.kaptn - X11/KDE GUI for EMBOSS 2.4 Message-ID: <200205171357.56451.sgmd@genetik.fu-berlin.de> Dear EMBOSS users, the latest version of the Kaptain user interface for EMBOSS is ready for download. EMBOSS.kaptn 0.78 supports all applications of EMBOSS 2.4.1 and some of the embossified Phylip 3.5. As usual, you will find a compressed tar archive for download, additional information, and a few screenshots at http://userpage.fu-berlin.de/~sgmd . From the ChangeLog: Version 0.78 - Finished support for EMBOSS 2.4 - report output for marscan.kaptn, patmatdb.kaptn, patmatmotifs.kaptn equicktandem.kaptn, etandem.kaptn - removed staden option from dbi*.kaptn - renamed -filename to -filenames in dbiblast.kaptn - fix for fuzztran.kaptn, fuzznuc.kaptn, fuzzpro.kaptn - new: yank.kaptn, union.kaptn Version 0.77 - new: tranalign.kaptn - fields and maxindex qualifiers for dbiblast.kaptn, dbifasta.kaptn, dbigcg.kaptn, dbiflat.kaptn - exclude qualifier for dbiblast.kaptn, dbigcg.kaptn - report output for fuzztran.kaptn, fuzznuc.kaptn, fuzzpro.kaptn Version 0.76 -new: eprotdist.kaptn, ednadist.kaptn, egendist.kaptn, eseqboot.kaptn efactor.kaptn, edollop.kaptn, ednainvar.kaptn Version 0.75 - better design for eneighbor.kaptn, ekitsch.kaptn - new: efitch.kaptn, epenny.kaptn, edolpenny.kaptn Version 0.74 - small fix in merger.kaptn & megamerger.kaptn, replace "-stout" by "-outfile stdout" - new: eneighbor.kaptn Version 0.73 - starting ephylip - new: ednapars.kaptn, ednapenny.kaptn, emix.kaptn eprotpars.kaptn, erestml.kaptn, ekitsch.kaptn Please let me know if I missed something in EMBOSS 2.4, that changelog was a bit longer than usual. Have a nice weekend Thomas -- Thomas Siegmund Freie Universit?t Berlin Institut f?r Genetik Arnimallee 7 14195 Berlin Germany Tel: +49 30 838 54868 Fax: +49 30 838 54395 http://userpage.fu-berlin.de/~sgmd From daniel at mrc-lmb.cam.ac.uk Fri May 17 13:03:11 2002 From: daniel at mrc-lmb.cam.ac.uk (Daniel Schlieper) Date: Fri, 17 May 2002 14:03:11 +0100 (BST) Subject: seqed? Message-ID: Hello, I really like emboss, and I use it as much as I can. In fact, the only reason to start a GCG session is seqed. I couldn't find anything like it in emboss. tfm newseq writes: "You wouldn't want to type a long sequence in by hand, anyway, would you?" Maybe I am old fashioned, but yes, I do. As I can type quickly, 1000 nt are not a problem, and sometimes the only way to get the sequence file. But this can only be done with a program that not only allows to type in nucleotides, but also to check them, to look for given sequences and so on. It will be even more helpfulll if it ignores blanks, carriage returns and numbers (for cut-and-paste). So I would be glad if you please add a seqed clone to the emboss suite. Best regards, Daniel -- Daniel Schlieper MRC Laboratory of Molecular Biology daniel at mrc-lmb.cam.ac.uk Hills Road, Cambridge CB2 2QH, UK Tel.: +44 1223 252969 FAX: +44 1223 213556 WWW: http://www2.mrc-lmb.cam.ac.uk/groups/JYL/index.html From gwilliam at hgmp.mrc.ac.uk Fri May 17 13:06:43 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Fri, 17 May 2002 14:06:43 +0100 Subject: seqed? References: Message-ID: <3CE50063.4459056@hgmp.mrc.ac.uk> Try 'mse http://www.uk.embnet.org/Software/EMBOSS/EMBASSY/MSE/mse.html This is an EMBASSY program, so has to be set up separately to the main EMBOSS distribution, which is why you may not have seen it. Gary Daniel Schlieper wrote: > > Hello, > > I really like emboss, and I use it as much as I can. In fact, the only > reason to start a GCG session is seqed. I couldn't find anything like it > in emboss. tfm newseq writes: "You wouldn't want to type a long sequence > in by hand, anyway, would you?" Maybe I am old fashioned, but yes, I do. > As I can type quickly, 1000 nt are not a problem, and sometimes the only > way to get the sequence file. > > But this can only be done with a program that not only allows to type in > nucleotides, but also to check them, to look for given sequences > and so on. It will be even more helpfulll if it ignores blanks, carriage > returns and numbers (for cut-and-paste). > > So I would be glad if you please add a seqed clone to the emboss suite. > > Best regards, Daniel > > -- > Daniel Schlieper MRC Laboratory of Molecular Biology > daniel at mrc-lmb.cam.ac.uk Hills Road, Cambridge CB2 2QH, UK > Tel.: +44 1223 252969 FAX: +44 1223 213556 > WWW: http://www2.mrc-lmb.cam.ac.uk/groups/JYL/index.html -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From daniel at mrc-lmb.cam.ac.uk Fri May 17 13:36:21 2002 From: daniel at mrc-lmb.cam.ac.uk (Daniel Schlieper) Date: Fri, 17 May 2002 14:36:21 +0100 (BST) Subject: seqed? In-Reply-To: <3CE50063.4459056@hgmp.mrc.ac.uk> Message-ID: Dear Gary, thank you very much. Yes mse is a bit hidden, but Peter Rice was as kind as to point me to that. In total, mse seems to be much better than seqed, and I will be happy to use it. Just in case if there is anybody interested in even improving it, there might two minor improvments possible: 1. There could be a check feature as in seqed. For example (from seqed): aacgggttaaggcct ^ ^^^^ aaccggttaaccggt ....|.........|.........|.... 0 10 20 2. There could be a way to read an empty (or not yet existing file). Now it says: Unix % mse i.seq Multiple Sequence Editor Error: failed to open filename i.seq Error: Unable to read sequence 'i.seq' Many thanks and best regards, Daniel -- Daniel Schlieper MRC Laboratory of Molecular Biology daniel at mrc-lmb.cam.ac.uk Hills Road, Cambridge CB2 2QH, UK Tel.: +44 1223 252969 FAX: +44 1223 213556 WWW: http://www2.mrc-lmb.cam.ac.uk/groups/JYL/index.html On Fri, 17 May 2002, Gary Williams, Tel 01223 494522 wrote: > > Try 'mse > http://www.uk.embnet.org/Software/EMBOSS/EMBASSY/MSE/mse.html > > This is an EMBASSY program, so has to be set up separately to the main > EMBOSS distribution, which is why you may not have seen it. > > Gary > > Daniel Schlieper wrote: > > > > Hello, > > > > I really like emboss, and I use it as much as I can. In fact, the only > > reason to start a GCG session is seqed. I couldn't find anything like it > > in emboss. tfm newseq writes: "You wouldn't want to type a long sequence > > in by hand, anyway, would you?" Maybe I am old fashioned, but yes, I do. > > As I can type quickly, 1000 nt are not a problem, and sometimes the only > > way to get the sequence file. > > > > But this can only be done with a program that not only allows to type in > > nucleotides, but also to check them, to look for given sequences > > and so on. It will be even more helpfulll if it ignores blanks, carriage > > returns and numbers (for cut-and-paste). > > > > So I would be glad if you please add a seqed clone to the emboss suite. > > > > Best regards, Daniel > > > > -- > > Daniel Schlieper MRC Laboratory of Molecular Biology > > daniel at mrc-lmb.cam.ac.uk Hills Road, Cambridge CB2 2QH, UK > > Tel.: +44 1223 252969 FAX: +44 1223 213556 > > WWW: http://www2.mrc-lmb.cam.ac.uk/groups/JYL/index.html > > -- > Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 > mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ > Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK > > From peter.rice at uk.lionbioscience.com Fri May 17 13:57:02 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 17 May 2002 14:57:02 +0100 Subject: seqed? References: Message-ID: <3CE50C2E.2C1D0ACF@uk.lionbioscience.com> Daniel Schlieper wrote: > > thank you very much. Yes mse is a bit hidden, but Peter Rice was as kind > as to point me to that. In total, mse seems to be much better than seqed, > and I will be happy to use it. > > Just in case if there is anybody interested in even improving it, there > might two minor improvments possible: > > 1. There could be a check feature as in seqed. For example (from seqed): > > aacgggttaaggcct > ^ ^^^^ > aaccggttaaccggt > ....|.........|.........|.... > 0 10 20 Aaaahhhhh .... that is rather nasty to implement. In SEQED it was really there for people typing in data from sequencing gels, and in particular for the "digitizer" input (a digitizer was a table with a pen where you clicked the pen tip on the 4 corners, on the lanes, and then on each band). The check mode was to compare two runs in order to catch clicks that were in between bands. Far simpler is to simply enter the sequence twice, then use wordmatch to compare them (again, that is basically what I used to do with SEQED anyway). > 2. There could be a way to read an empty (or not yet existing file). Now > it says: > > Unix % mse i.seq > Multiple Sequence Editor > Error: failed to open filename i.seq > Error: Unable to read sequence 'i.seq' That one is a simple EMBOSS global change, allowing an input "sequence set" to be empty. Basically, adding the nullok attribute for sequences, or perhaps a minimum number of sequences for a sequence set (default 1, emma would like more, mse could handle 0). Expect something in a future release. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From tmargus at ebc.ee Mon May 20 16:00:15 2002 From: tmargus at ebc.ee (=?iso-8859-1?Q?T=F5nu_Margus?=) Date: Mon, 20 May 2002 19:00:15 +0300 Subject: installing EMBOSS 2.4.1 and EMBASSY Message-ID: <00d701c20017$c1c47240$1e1728c1@ebc.ee> Hi, First problem installing EMBOSS ( op-sys LINUX slackware 8.0) ./configure runs ok but make gives an error % make .......... gcc -g -O2 -o .libs/abiview abiview.o ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so ../ajax/.libs/libajax.so ../plplot/.libs/libplplot.so -L/usr/X11R6/lib -lX11 -lm -Wl,--rpath -Wl,/usr/local/bin1/emboss/lib ../plplot/.libs/libplplot.so: undefined reference to `atexit' collect2: ld returned 1 exit status make[2]: *** [abiview] Error 1 in some reason it didn't find atexit so I comment it out from plplot/tek.c /*#ifdef STDC_HEADERS if (atexit(tty_atexit)) (void) fprintf(stderr, "Unable to set up atexit handler.\n"); #endif*/ return; Now it compiles without problems Second problem arouse when I tried to install MEME ./configure didn't find the file ./../../ltconfig cd /programs/EMBOSS-2.4.1/embassy/MEME-2.3.1/ ./configure --prefix=/usr/local/bin1/emboss updating cache ./config.cache ./../../ltconfig: ./../../ltconfig: No such file or directory configure: error: libtool configure failed Same problems appears with MSE-0.0.4 PHYLIP and HMMER installed without problems. Sincerely yours Tonu Margus Estonian Biocenter & Tartu University Riia 23 Tartu 51010 Estonia E-mail tmargus at ebc.ee -------------- next part -------------- An HTML attachment was scrubbed... URL: From ekolomiets at yahoo.com Wed May 22 17:13:59 2002 From: ekolomiets at yahoo.com (Elena Kolomiets) Date: Wed, 22 May 2002 10:13:59 -0700 (PDT) Subject: Database set up Q's Message-ID: <20020522171359.43290.qmail@web13805.mail.yahoo.com> Hello, i am looking for detaile description of whow to set up my oun Database definition. How .embossrc and .embossdata works along with emboss.default? My showdb result in listing test databases even though the emboss_tempdata variable commented in emboss.default file???!!! ===== Sincerely, Elena Kolomiets 3927 Hawk Owl Cove, College Station, TX 77845 (979)690-3172 __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From ekolomiets at yahoo.com Wed May 22 17:44:52 2002 From: ekolomiets at yahoo.com (Elena Kolomiets) Date: Wed, 22 May 2002 10:44:52 -0700 (PDT) Subject: Database set up Q's Message-ID: <20020522174452.50118.qmail@web13805.mail.yahoo.com> Hello, i am looking for detaile description of whow to set up my oun Database definition. How .embossrc and .embossdata works along with emboss.default? My showdb result in listing test databases even though the emboss_tempdata variable commented in emboss.default file???!!! ===== Sincerely, Elena Kolomiets 3927 Hawk Owl Cove, College Station, TX 77845 (979)690-3172 __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From David.Bauer at SCHERING.DE Thu May 23 05:48:58 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Thu, 23 May 2002 07:48:58 +0200 Subject: Antwort: Database set up Q's Message-ID: Hi, there is a very usefull adminguide written by David Martin at http://www.uk.embnet.org/Software/EMBOSS/admin.html It contains a detailed description of setting up databases to work with emboss. David. Hello, i am looking for detaile description of whow to set up my oun Database definition. How .embossrc and .embossdata works along with emboss.default? My showdb result in listing test databases even though the emboss_tempdata variable commented in emboss.default file???!!! ===== Sincerely, Elena Kolomiets 3927 Hawk Owl Cove, College Station, TX 77845 (979)690-3172 __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From gwilliam at hgmp.mrc.ac.uk Thu May 23 08:18:26 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 23 May 2002 09:18:26 +0100 Subject: Antwort: Database set up Q's References: Message-ID: <3CECA5D2.D4DA1166@hgmp.mrc.ac.uk> See also the description of the database specification syntax at: http://www.uk.embnet.org/Software/EMBOSS/Usa/databases.html Gary David.Bauer at SCHERING.DE wrote: > > Hi, > > there is a very usefull adminguide written by David Martin at > > http://www.uk.embnet.org/Software/EMBOSS/admin.html > > It contains a detailed description of setting up databases to work with emboss. > > David. > > Hello, > i am looking for detaile description of whow to set up > > my oun Database definition. > How .embossrc and .embossdata works along with > emboss.default? > My showdb result in listing test databases even though > the emboss_tempdata variable commented in > emboss.default file???!!! > > ===== > Sincerely, > > Elena Kolomiets > 3927 Hawk Owl Cove, > College Station, TX 77845 > (979)690-3172 > > __________________________________________________ > Do You Yahoo!? > LAUNCH - Your Yahoo! Music Experience > http://launch.yahoo.com -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From peter.rice at uk.lionbioscience.com Thu May 23 08:22:24 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 23 May 2002 09:22:24 +0100 Subject: Database set up Q's References: <20020522171359.43290.qmail@web13805.mail.yahoo.com> Message-ID: <3CECA6C0.EC5FC4DF@uk.lionbioscience.com> Elena Kolomiets wrote: > > i am looking for detaile description of whow to set up > > my oun Database definition. > How .embossrc and .embossdata works along with > emboss.default? > My showdb result in listing test databases even though > the emboss_tempdata variable commented in > emboss.default file???!!! You need to comment out the DB lines for the test databases to remove them. Commenting out emboss_tempdata means the test databases are still defined, but will not work. I am working on adding more comments to emboss.default.template and updating the Admin Guide and web pages. Of course, updating emboss.default.template may not help users who already have their own emboss.default file so we can make comments in the next release notes too to make sure they see the updates. regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From dmamartin at dundee.ac.uk Thu May 23 08:28:49 2002 From: dmamartin at dundee.ac.uk (David Martin) Date: Thu, 23 May 2002 09:28:49 +0100 (BST) Subject: Antwort: Database set up Q's In-Reply-To: <3CECA5D2.D4DA1166@hgmp.mrc.ac.uk> Message-ID: On Thu, 23 May 2002, Gary Williams, Tel 01223 494522 wrote: > > See also the description of the database specification syntax at: > http://www.uk.embnet.org/Software/EMBOSS/Usa/databases.html > There have been a number of changes in EMBOSS that add more functionality to the database definitions since the admin guide was last updated by me. Everything in the admin guide is more or less valid (some of the platform specific stuff is a bit dated, ie OS X and IRIX may not be entirely correct now) but misses some of the new bits. Peter Rice has picked up the poisoned chalice of updating the admin guide (probably so I don't fill his email inbox with stupid questions again) and it will be released under a free documentation license in due course. The existing version will get you going for now and is 99% compatible with todays EMBOSS but only covers 75% of the features. ..d ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee +44 1382 348704 9f:2e:d8:b6:fb:fd:2c:77:02:50:ea:c0:d6:af:04:ed ---------------------------------- From peter.rice at uk.lionbioscience.com Thu May 23 08:45:38 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 23 May 2002 09:45:38 +0100 Subject: Database set up Q's References: Message-ID: <3CECAC32.1719C672@uk.lionbioscience.com> David Martin wrote: > > Peter Rice has picked up the poisoned chalice of updating the admin guide > (probably so I don't fill his email inbox with stupid questions again) and > it will be released under a free documentation license in due course. > > The existing version will get you going for now and is 99% compatible with > todays EMBOSS but only covers 75% of the features. So, the obvious request .... please send me all your stupid questions that the Admin Guide should be able to answer. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From p.lopriore at it.ibm.com Fri May 24 16:07:54 2002 From: p.lopriore at it.ibm.com (Pietro Lopriore) Date: Fri, 24 May 2002 18:07:54 +0200 Subject: No subject Message-ID: Hi everybody, a short question: is there a method (a command-line option) so that EMBOSS doesn't write any output result file? I would like to obtain my results in the stdoutput without writing on the file system. Thanks in advance Best regards Pietro _________________________________________________ Pietro Lopriore IBM Java Technology Center via Tridente 42/14 - 70125 BARI - ITALY Tel. +39 .80.5466715 - Fax. +39.80.5466621 Tie Line: 37715 email: p.lopriore at it.ibm.com Web Site: http://www.ibm.com/it/semeasud From peter.rice at uk.lionbioscience.com Fri May 24 16:06:58 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 24 May 2002 17:06:58 +0100 Subject: stdout output References: Message-ID: <3CEE6522.BDE96F72@uk.lionbioscience.com> Pietro Lopriore wrote: > > Hi everybody, > a short question: > is there a method (a command-line option) so that EMBOSS doesn't write any > output result file? > I would like to obtain my results in the stdoutput without writing on the > file system. -stdout will default to standard output for all applications -filter will default to standard input and standard output for all applications (and also, because standard input is in use, defaults to -auto) Some folk (Alan for example) like to define these globally, for example: setenv EMBOSS_STDOUT Y You can put this in your login, or in your .embossrc file This applies only to the first output file. Any secondary output goes to a file. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From simon.andrews at bbsrc.ac.uk Tue May 28 08:40:46 2002 From: simon.andrews at bbsrc.ac.uk (simon andrews (BI)) Date: Tue, 28 May 2002 09:40:46 +0100 Subject: Bug in seqret in EMBOSS 2.4.1 ? Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E2859C@bi-exsrv1.iapc.bbsrc.ac.uk> I think I've found a problem with seqret in v2.4.1. It's failing to fetch sequences from EBIs SRS system, which fetch fine when I use seqret from v2.2.0. My setup in emboss.default is this: DB embl [ type: N method: url format: embl url: "http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[EMBLRELEASE-ACC:%s]" comment: "EBI EMBL ACs" ] Using this under 2.4.1 produces: $ seqret embl:z83307 Reads and writes (returns) sequences Error: Unable to read sequence 'embl:z83307' $ ...and the same thing under 2.2.0 gives: $ seqret embl:z83307 Reads and writes (returns) sequences Output sequence [hsa1280.fasta]: $ Running the latest seqret with -debug shows that the sequence is fetched (you can see it being parsed), but that it is the format recognition at the end which fails. The last bits of the debug file are at the bottom of this message. Is this a bug in seqret, or do I need to update the format of my emboss.default file? Thanks for any help Simon. ################################## :[1] agatgaaaaa ggggagaacc atattatttt ggtcaaaata ttgtggtcca caagcatatg 21960 :[1] ctccagttag tttctttctt gaataaaggc tttttattgt catgtaaaca caagctgtgt 22020 :[1] gcacatgatc aaaatatttt aaaactaaaa ataatttatg aaaaaatatt cttccttgat 22080 :[1] ttcaacctgc ctgtacttat ttttaataca aatatatcta ggataaaaga tactattata 22140 :[1] caaatgcatg atcaaggaag atgtcagaaa ggttaacggg gtcaagaaaa gctgtaacac 22200 :[1] tcatagagta atatccatac agaactattc cttagtatcc atgggaccca gcc 22253 :[1] // removing '' [1] leaving ''' ' [1] [1] :[1] 0 [1] seqRead: seqin format 3 'embl' ajFeattableDel 0 ajFileBuffNoBuff buffsize: 492 ++seqRead known format 3 ++seqReadFmt format 3 (embl) 'embl:z83307' feat No seqReadEmbl first line '620 ' Format 3 (embl) failed, file buffer reset by seqReadFmt ++seqReadFmt failed - nothing read seqRead: (b2) seqReadFmt stat == FAIL *failed* ajFeattableDel 0 seqRead failed - try again with format 3 'embl' ++seqReadFmt format 3 (embl) 'embl:z83307' feat No seqReadEmbl first line '620 ' Format 3 (embl) failed, file buffer reset by seqReadFmt ++seqReadFmt failed - nothing read seqRead: (b3) seqReadFmt stat == FAIL *failed* Failure for option 'sequence' From peter.rice at uk.lionbioscience.com Tue May 28 10:21:35 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 28 May 2002 11:21:35 +0100 Subject: Bug in seqret in EMBOSS 2.4.1 ? References: <2DC41140A89ED411989D00508BDCD9ED01E2859C@bi-exsrv1.iapc.bbsrc.ac.uk> Message-ID: <3CF35A2F.53761480@uk.lionbioscience.com> Hi Simon, > I think I've found a problem with seqret in v2.4.1. It's failing to fetch > sequences from EBIs SRS system, which fetch fine when I use seqret from > v2.2.0. Tricky one ... your definition works fine for me. Can you send the full seqret.dbg file from 2.4.1 and from 2.2.0 regards, Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From krishna at mrna.tn.nic.in Tue May 28 10:32:05 2002 From: krishna at mrna.tn.nic.in (Krishnaswamy S) Date: Tue, 28 May 2002 16:02:05 +0530 (IST) Subject: patmatdb Message-ID: we wish to modify the patmatdb program be modified to search for say 70% similarity to the prosite pattern. How can this be done? Is there a c program source of the prosite scan program available? regards krishnaswamy -- S.Krishnaswamy School of Biotechnology Madurai Kamaraj University Madurai 625 021, India mkubic9 at giasmd01.vsnl.net.in krishna at mrna.tn.nic.in From krishna at mrna.tn.nic.in Tue May 28 10:33:47 2002 From: krishna at mrna.tn.nic.in (Krishnaswamy S) Date: Tue, 28 May 2002 16:03:47 +0530 (IST) Subject: patmatdb - without typos Message-ID: we wish to modify the patmatdb program to search for say 70% similarity to the prosite pattern. How can this be done? Is there a c program source of the prosite scan program available? regards krishnaswamy -- S.Krishnaswamy School of Biotechnology Madurai Kamaraj University Madurai 625 021, India mkubic9 at giasmd01.vsnl.net.in krishna at mrna.tn.nic.in