From foisys at medcn.umontreal.ca Mon Jun 4 10:59:55 2001 From: foisys at medcn.umontreal.ca (Sylvain Foisy, Ph. D.) Date: Mon, 4 Jun 2001 10:59:55 -0400 Subject: Running EMBOSS in Mac OS X Message-ID: <000801c0ed07$0c2f6300$2f30340a@chum.rr06.rtss> Hi, I am new to this mailing list so this question might already have been answered. I just installed OS X on my G4 mimitower and I would like to use a good sequence analysis software to learn some programming. I read on MacCentral that someone had been able to run EMBOSS under OS X. Anybody has some experience? Cordially Sylvain Foisy, Ph. D. Research Assciate Molecular Nutrition Unit Research Center CHUM Hopital Notre-Dame 1560 East Sherbrooke St Montreal,QC H2L 4M1 Phone: (514) 281-6000 x.8872 Fax: (514) 896-4689 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20010604/5036b3fb/attachment.html From gwilliam at hgmp.mrc.ac.uk Mon Jun 4 11:13:15 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Mon, 04 Jun 2001 16:13:15 +0100 Subject: Running EMBOSS in Mac OS X References: <000801c0ed07$0c2f6300$2f30340a@chum.rr06.rtss> Message-ID: <3B1BA58B.227820D6@hgmp.mrc.ac.uk> > "Sylvain Foisy, Ph. D." wrote: > > Hi, > > I am new to this mailing list so this question might already have been > answered. I just installed OS X on my G4 mimitower and I would like > to use a good sequence analysis software to learn some programming. I > read on MacCentral that someone had been able to run EMBOSS under OS > X. Anybody has some experience? I will send you some of the messages that we have had on this list about installing under OS X. Gary -- 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 ableasby at hgmp.mrc.ac.uk Sat Jun 9 17:18:09 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sat, 9 Jun 2001 22:18:09 +0100 (BST) Subject: EMBOSS 1.13.2 Message-ID: <200106092118.WAA18683@bromine.hgmp.mrc.ac.uk> This contains bugfixes for REMAP, DBIGCG, DBIBLAST and PEPWINDOW which were introduced by a code reorganisation in 1.13.0. The configuration also supports a wider range of libgd installations on SGI systems (those with math library calls included). An additional program is: CUTGEXTRACT: given the name of a directory containing the CUTG database (ftp://ftp.ebi.ac.uk/pub/databases/cutg) this will calculate codon usage tables for individual species (e.g. EHomo_sapiens.cut) and place them in the CODONS subdirectory of the EMBOSS data directory. This is an all-or-nothing extraction, will create many files and take several minutes. The usage tables are from the sum of codons over all sequences for each organism. The above program is to be regarded as a release to satisfy demand; it is intended to build the code into the EMBOSS libraries shortly. The codon usage tables provided with the distribution are calculated from the files in (ftp://ftp.ebi.ac.uk/pub/databases/codonusage) with a few additions whose exact derivation cannot easily be determined. They will be replaced in future releases by a selection of files derived from CUTG. As usual, you can specify a required codon usage file using one of the application options. The bulk of the code for EMBOSS version 2 has been committed and we are currently modifying applications to make use of new feature handling and report code. Alan From David.Lapointe at umassmed.edu Mon Jun 11 17:37:53 2001 From: David.Lapointe at umassmed.edu (Lapointe, David) Date: Mon, 11 Jun 2001 17:37:53 -0400 Subject: IRIX CC quirks Message-ID: 1.13.2 compiled fine with gcc/Linux but I had some fatal errors show up in dbifasta.c and dbiflat.c using IRIX and CC ( MIPSPro C). In both files exclude is defined AjPStr exclude; then later exclude= ajAcdGetString("exclude"); This is incompatible with the way it is used in embDbiFileList where exclude has the AjBool type. Should this be embDbiFileListExc in these two files? David ----- David Lapointe UMassMedicalSchool/Worcester MA "Great minds think a lot" From ableasby at hgmp.mrc.ac.uk Tue Jun 12 08:31:47 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 12 Jun 2001 13:31:47 +0100 (BST) Subject: EMBOSS 1.13.3 Message-ID: <200106121231.NAA24671@bromine.hgmp.mrc.ac.uk> Fixes the exclusion/compilation error in DBIFASTA & DBIFLAT. Alan From gen184 at abdn.ac.uk Tue Jun 19 10:53:30 2001 From: gen184 at abdn.ac.uk (caroline barelle) Date: Tue, 19 Jun 2001 15:53:30 +0100 (BST) Subject: protein alignment Message-ID: I am currently trying to obtain % identity between a number of proteins within a family (I need identity along the whole length of the protein). Is there a package I can use to achieve this? ---------------------- Dr Caroline Barelle Department of Molecular and Cell Biology Institute of Medical Sciences Foresterhill Aberdeen AB25 2ZD c.j.barelle at abdn.ac.uk From dmartin at bioinformatics.msiwtb.dundee.ac.uk Wed Jun 20 04:33:07 2001 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Wed, 20 Jun 2001 09:33:07 +0100 (BST) Subject: Features and properties.. Message-ID: Just a quick question.. Will the eagerly anticipated new code for features etc. allow the extraction by species from a database? ..d From peter.rice at uk.lionbioscience.com Wed Jun 20 04:40:59 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 20 Jun 2001 09:40:59 +0100 Subject: Features and properties.. References: Message-ID: <3B30619B.11359D7D@uk.lionbioscience.com> David Martin wrote: > > Will the eagerly anticipated new code for features etc. allow the > extraction by species from a database? No - it will read features, but what you want is a separate species index. It would be possible to add other fields to the USA. So far it has id and acc, and also has a partial definition for 'des' (as in swissprot-des:kinase) although it has not been implemented. Obviously this will only apply to indexed databases. Using SRS it is easy to request a species. The EMBOSS 'emblcd' indices can also have a species index by extending the dbi programs. The changes needed are not many. What is the need? One obvious problem would be how to support more complex queries than "swissprot-org:caenorhabditis elegans" and how to cope with spaces in USAs. -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From dmartin at bioinformatics.msiwtb.dundee.ac.uk Mon Jun 25 05:43:48 2001 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Mon, 25 Jun 2001 10:43:48 +0100 (BST) Subject: EMBOSS on Mac OS X Message-ID: Dear all EMBOSSers, I have finally got a Mac and worked through the installation of EMBOSS on OS X. The good news: EMBOSS will install and run with full functionality on OS X. The bad news: Due to a number of missing libraries and other issues, installation is not as straightforward as one would like. The good news: Full details are in the latest version of the Admin guide. For reasons outside of my control I no longer have access to an anonymous FTP server so I have forwarded the LaTeX, PS, and PDF versions to Gary to put up on the main site. Even better news: It is rumoured that Mac OS X will be adopting the FreeBSD ports system (or a variant thereof) which will in future allow instalaltion with a lot less hassle. Credits: Many thanks to Don Gilbert for the initial advice on getting EMBOSS to configure correctly. Gary will announce a URL when he has put the latest version of the admin guide up. ..d David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, University of Dundee From gwilliam at hgmp.mrc.ac.uk Wed Jun 27 08:19:15 2001 From: gwilliam at hgmp.mrc.ac.uk (gwilliam at hgmp.mrc.ac.uk) Date: Wed, 27 Jun 2001 13:19:15 +0100 (BST) Subject: EMBOSS admin guide update Message-ID: <200106271219.NAA12250@californium.hgmp.mrc.ac.uk> The EMBOSS admin guide by David Martin has been updated. See: http://www.uk.embnet.org/Software/EMBOSS/Doc/Admin_guide/adminguide/ 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 foisys at medcn.umontreal.ca Mon Jun 4 14:59:55 2001 From: foisys at medcn.umontreal.ca (Sylvain Foisy, Ph. D.) Date: Mon, 4 Jun 2001 10:59:55 -0400 Subject: Running EMBOSS in Mac OS X Message-ID: <000801c0ed07$0c2f6300$2f30340a@chum.rr06.rtss> Hi, I am new to this mailing list so this question might already have been answered. I just installed OS X on my G4 mimitower and I would like to use a good sequence analysis software to learn some programming. I read on MacCentral that someone had been able to run EMBOSS under OS X. Anybody has some experience? Cordially Sylvain Foisy, Ph. D. Research Assciate Molecular Nutrition Unit Research Center CHUM Hopital Notre-Dame 1560 East Sherbrooke St Montreal,QC H2L 4M1 Phone: (514) 281-6000 x.8872 Fax: (514) 896-4689 -------------- next part -------------- An HTML attachment was scrubbed... URL: From gwilliam at hgmp.mrc.ac.uk Mon Jun 4 15:13:15 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Mon, 04 Jun 2001 16:13:15 +0100 Subject: Running EMBOSS in Mac OS X References: <000801c0ed07$0c2f6300$2f30340a@chum.rr06.rtss> Message-ID: <3B1BA58B.227820D6@hgmp.mrc.ac.uk> > "Sylvain Foisy, Ph. D." wrote: > > Hi, > > I am new to this mailing list so this question might already have been > answered. I just installed OS X on my G4 mimitower and I would like > to use a good sequence analysis software to learn some programming. I > read on MacCentral that someone had been able to run EMBOSS under OS > X. Anybody has some experience? I will send you some of the messages that we have had on this list about installing under OS X. Gary -- 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 ableasby at hgmp.mrc.ac.uk Sat Jun 9 21:18:09 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sat, 9 Jun 2001 22:18:09 +0100 (BST) Subject: EMBOSS 1.13.2 Message-ID: <200106092118.WAA18683@bromine.hgmp.mrc.ac.uk> This contains bugfixes for REMAP, DBIGCG, DBIBLAST and PEPWINDOW which were introduced by a code reorganisation in 1.13.0. The configuration also supports a wider range of libgd installations on SGI systems (those with math library calls included). An additional program is: CUTGEXTRACT: given the name of a directory containing the CUTG database (ftp://ftp.ebi.ac.uk/pub/databases/cutg) this will calculate codon usage tables for individual species (e.g. EHomo_sapiens.cut) and place them in the CODONS subdirectory of the EMBOSS data directory. This is an all-or-nothing extraction, will create many files and take several minutes. The usage tables are from the sum of codons over all sequences for each organism. The above program is to be regarded as a release to satisfy demand; it is intended to build the code into the EMBOSS libraries shortly. The codon usage tables provided with the distribution are calculated from the files in (ftp://ftp.ebi.ac.uk/pub/databases/codonusage) with a few additions whose exact derivation cannot easily be determined. They will be replaced in future releases by a selection of files derived from CUTG. As usual, you can specify a required codon usage file using one of the application options. The bulk of the code for EMBOSS version 2 has been committed and we are currently modifying applications to make use of new feature handling and report code. Alan From David.Lapointe at umassmed.edu Mon Jun 11 21:37:53 2001 From: David.Lapointe at umassmed.edu (Lapointe, David) Date: Mon, 11 Jun 2001 17:37:53 -0400 Subject: IRIX CC quirks Message-ID: 1.13.2 compiled fine with gcc/Linux but I had some fatal errors show up in dbifasta.c and dbiflat.c using IRIX and CC ( MIPSPro C). In both files exclude is defined AjPStr exclude; then later exclude= ajAcdGetString("exclude"); This is incompatible with the way it is used in embDbiFileList where exclude has the AjBool type. Should this be embDbiFileListExc in these two files? David ----- David Lapointe UMassMedicalSchool/Worcester MA "Great minds think a lot" From ableasby at hgmp.mrc.ac.uk Tue Jun 12 12:31:47 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 12 Jun 2001 13:31:47 +0100 (BST) Subject: EMBOSS 1.13.3 Message-ID: <200106121231.NAA24671@bromine.hgmp.mrc.ac.uk> Fixes the exclusion/compilation error in DBIFASTA & DBIFLAT. Alan From gen184 at abdn.ac.uk Tue Jun 19 14:53:30 2001 From: gen184 at abdn.ac.uk (caroline barelle) Date: Tue, 19 Jun 2001 15:53:30 +0100 (BST) Subject: protein alignment Message-ID: I am currently trying to obtain % identity between a number of proteins within a family (I need identity along the whole length of the protein). Is there a package I can use to achieve this? ---------------------- Dr Caroline Barelle Department of Molecular and Cell Biology Institute of Medical Sciences Foresterhill Aberdeen AB25 2ZD c.j.barelle at abdn.ac.uk From dmartin at bioinformatics.msiwtb.dundee.ac.uk Wed Jun 20 08:33:07 2001 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Wed, 20 Jun 2001 09:33:07 +0100 (BST) Subject: Features and properties.. Message-ID: Just a quick question.. Will the eagerly anticipated new code for features etc. allow the extraction by species from a database? ..d From peter.rice at uk.lionbioscience.com Wed Jun 20 08:40:59 2001 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 20 Jun 2001 09:40:59 +0100 Subject: Features and properties.. References: Message-ID: <3B30619B.11359D7D@uk.lionbioscience.com> David Martin wrote: > > Will the eagerly anticipated new code for features etc. allow the > extraction by species from a database? No - it will read features, but what you want is a separate species index. It would be possible to add other fields to the USA. So far it has id and acc, and also has a partial definition for 'des' (as in swissprot-des:kinase) although it has not been implemented. Obviously this will only apply to indexed databases. Using SRS it is easy to request a species. The EMBOSS 'emblcd' indices can also have a species index by extending the dbi programs. The changes needed are not many. What is the need? One obvious problem would be how to support more complex queries than "swissprot-org:caenorhabditis elegans" and how to cope with spaces in USAs. -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From dmartin at bioinformatics.msiwtb.dundee.ac.uk Mon Jun 25 09:43:48 2001 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Mon, 25 Jun 2001 10:43:48 +0100 (BST) Subject: EMBOSS on Mac OS X Message-ID: Dear all EMBOSSers, I have finally got a Mac and worked through the installation of EMBOSS on OS X. The good news: EMBOSS will install and run with full functionality on OS X. The bad news: Due to a number of missing libraries and other issues, installation is not as straightforward as one would like. The good news: Full details are in the latest version of the Admin guide. For reasons outside of my control I no longer have access to an anonymous FTP server so I have forwarded the LaTeX, PS, and PDF versions to Gary to put up on the main site. Even better news: It is rumoured that Mac OS X will be adopting the FreeBSD ports system (or a variant thereof) which will in future allow instalaltion with a lot less hassle. Credits: Many thanks to Don Gilbert for the initial advice on getting EMBOSS to configure correctly. Gary will announce a URL when he has put the latest version of the admin guide up. ..d David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, University of Dundee From gwilliam at hgmp.mrc.ac.uk Wed Jun 27 12:19:15 2001 From: gwilliam at hgmp.mrc.ac.uk (gwilliam at hgmp.mrc.ac.uk) Date: Wed, 27 Jun 2001 13:19:15 +0100 (BST) Subject: EMBOSS admin guide update Message-ID: <200106271219.NAA12250@californium.hgmp.mrc.ac.uk> The EMBOSS admin guide by David Martin has been updated. See: http://www.uk.embnet.org/Software/EMBOSS/Doc/Admin_guide/adminguide/ 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