From jison at hgmp.mrc.ac.uk Tue Oct 9 07:17:04 2001 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Tue, 09 Oct 2001 12:17:04 +0100 Subject: Open Source Petition Message-ID: <3BC2DCB0.92830CE@hgmp.mrc.ac.uk> Not directly related to EMBOSS but very worthwhile indeed: http://www.openinformatics.org/dsp_petition.php Jon -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ CCP11 : http://www.hgmp.mrc.ac.uk/CCP11/ From jackl at cmbi.kun.nl Tue Oct 9 09:05:51 2001 From: jackl at cmbi.kun.nl (Jack Leunissen) Date: Tue, 9 Oct 2001 15:05:51 +0200 Subject: Open Source Petition In-Reply-To: <3BC2DCB0.92830CE@hgmp.mrc.ac.uk> Message-ID: > Not directly related to EMBOSS but > very worthwhile indeed: > > http://www.openinformatics.org/dsp_petition.php It displays a very interesting PHP file opening error indeed ;-) Cheers, Jack Jack A.M. Leunissen | Email: jackl at cmbi.kun.nl Centre for Molecular and | Tel. : +31 24 365 22 48 Biomolecular Informatics | Fax : +31 24 365 29 77 Nijmegen, The Netherlands | Www : http://www.cmbi.nl/ From bgibbon at email.arizona.edu Wed Oct 10 12:56:32 2001 From: bgibbon at email.arizona.edu (Bryan Gibbon) Date: Wed, 10 Oct 2001 09:56:32 -0700 Subject: Problems with emowse Message-ID: <3BC47DC0.597B5D37@email.arizona.edu> Hello, I am having some trouble with emowse searches of flatfile databases (NCBI format). When I perform a search the results are empty except for the list of masses used for the search. The database is indexed correctly as I can fetch any entry with seqret or entret. Searches against a fasta database returned by seqret and indexed with dbifasta work fine. Is there any way to make emowse read the flatfile databases properly so that I do not have to maintain a fasta copy of every protein database? Thanks in advance for your help, -- Bryan Gibbon Department of Plant Sciences University of Arizona 303 Forbes Tucson, AZ 85721 Phone: 520-621-9154 Fax: 520-621-3692 http://ag.arizona.edu/research/larkinslab/index.htm From heme at postmark.net Tue Oct 16 09:52:10 2001 From: heme at postmark.net (Per Johansson) Date: Tue, 16 Oct 2001 13:52:10 +0000 Subject: Default program settings Message-ID: <20011016135210.16005.qmail@venus.postmark.net> Hi, I have some problems to set default program settings. I tried to put set emboss_verbose 1 in the emboss.default file but it doesn't seem to work. The command setenv emboss_verbose 1 doesn't work either, suggestions? From cutler at tularik.com Wed Oct 17 17:01:26 2001 From: cutler at tularik.com (Gene Cutler) Date: Wed, 17 Oct 2001 14:01:26 -0700 Subject: trouble indexing fasta database Message-ID: I am trying to index a fasta database and then retrieve sequences with seqret. I used dbifasta on half of the human genome golden path from ensembl: dbifasta -idformat simple -dbname ensembl_gp1 -directory . -filenames 'ensembl_golden_path.1' -indexdirectory /scratch1/databases/emboss/ and put this in my emboss.default: DB ensembl_gp1 [ type: N method: emblcd format: fasta dir: /scratch1/databases/raw/ file: ensembl_golden_path.1 indexdir: /scratch1/databases/emboss/ ] If I try to fetch a sequence located in the beginning of the fasta file, it works fine. But sequences further into the file aren't retrieved: > seqret ensembl_gp1:AC007798.1.15164.16328 Reads and writes (returns) sequences An error has been found: EMBLCD Entry failed An error has been found: Database 'ensembl_gp1' : access method 'emblcd' failed An error has been found: option -sequence: Unable to read sequence 'ensembl_gp1:AC007798.1.15164.16328' There is a serious problem: seqret terminated: Bad value for option and no prompt However, when I tried retrieving all the sequences: > seqret ensembl_gp1:* I got them all back. I can also retrieve the sequences if I get them directly from the fasta file rather than using the index. That makes it seem to be an index problem. Recreating the indexes hasn't helped. From mbehnke at vmbmod10.msu.montana.edu Wed Oct 17 18:39:40 2001 From: mbehnke at vmbmod10.msu.montana.edu (Michael Behnke) Date: Wed, 17 Oct 2001 16:39:40 -0600 (MDT) Subject: getorf Message-ID: I have been using the getorf program recently to find ORF's in Cryptosporidium contigs with great results. I do have a question though. Does anyone know what are the STOP and START codons used by the program, and do they change depending upon the table one uses? I see that plotorf uses Stop codons = TAA,TAG,TGA and Start codon = ATG, are these the same for getorf? Thanks Mike Behnke Bioinformatics Tech White Lab Montana State University From gwilliam at hgmp.mrc.ac.uk Thu Oct 18 08:40:55 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 18 Oct 2001 13:40:55 +0100 Subject: getorf References: Message-ID: <3BCECDD7.E9F070C1@hgmp.mrc.ac.uk> Michael Behnke wrote: > > I have been using the getorf program recently to find ORF's in > Cryptosporidium contigs with great results. I do have a question though. > Does anyone know what are the STOP and START codons used by the program, > and do they change depending upon the table one uses? I see that plotorf > uses Stop codons = TAA,TAG,TGA and Start codon = ATG, are these the same > for getorf? Yes, the STOP & START codons are held in the genetic code tables and will change with the table you choose. By default this is the Standard Code (See http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c) The STOP & START codons in the default table are, as you describe above, Stop codons = TAA,TAG,TGA and Start codon = ATG. The '-table' qualifier allows you to pick other tables. 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 jison at hgmp.mrc.ac.uk Tue Oct 9 11:17:04 2001 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Tue, 09 Oct 2001 12:17:04 +0100 Subject: Open Source Petition Message-ID: <3BC2DCB0.92830CE@hgmp.mrc.ac.uk> Not directly related to EMBOSS but very worthwhile indeed: http://www.openinformatics.org/dsp_petition.php Jon -- Jon C. Ison, PhD Bioinformatics Applications Group UK MRC Human Genome Mapping Project Resource Centre Hinxton, Cambridge, CB10 1SB, UK E-mail : jison at hgmp.mrc.ac.uk Tel : 01223 49-4548 HGMP-RC: http://www.hgmp.mrc.ac.uk/ EMBOSS : http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ CCP11 : http://www.hgmp.mrc.ac.uk/CCP11/ From jackl at cmbi.kun.nl Tue Oct 9 13:05:51 2001 From: jackl at cmbi.kun.nl (Jack Leunissen) Date: Tue, 9 Oct 2001 15:05:51 +0200 Subject: Open Source Petition In-Reply-To: <3BC2DCB0.92830CE@hgmp.mrc.ac.uk> Message-ID: > Not directly related to EMBOSS but > very worthwhile indeed: > > http://www.openinformatics.org/dsp_petition.php It displays a very interesting PHP file opening error indeed ;-) Cheers, Jack Jack A.M. Leunissen | Email: jackl at cmbi.kun.nl Centre for Molecular and | Tel. : +31 24 365 22 48 Biomolecular Informatics | Fax : +31 24 365 29 77 Nijmegen, The Netherlands | Www : http://www.cmbi.nl/ From bgibbon at email.arizona.edu Wed Oct 10 16:56:32 2001 From: bgibbon at email.arizona.edu (Bryan Gibbon) Date: Wed, 10 Oct 2001 09:56:32 -0700 Subject: Problems with emowse Message-ID: <3BC47DC0.597B5D37@email.arizona.edu> Hello, I am having some trouble with emowse searches of flatfile databases (NCBI format). When I perform a search the results are empty except for the list of masses used for the search. The database is indexed correctly as I can fetch any entry with seqret or entret. Searches against a fasta database returned by seqret and indexed with dbifasta work fine. Is there any way to make emowse read the flatfile databases properly so that I do not have to maintain a fasta copy of every protein database? Thanks in advance for your help, -- Bryan Gibbon Department of Plant Sciences University of Arizona 303 Forbes Tucson, AZ 85721 Phone: 520-621-9154 Fax: 520-621-3692 http://ag.arizona.edu/research/larkinslab/index.htm From heme at postmark.net Tue Oct 16 13:52:10 2001 From: heme at postmark.net (Per Johansson) Date: Tue, 16 Oct 2001 13:52:10 +0000 Subject: Default program settings Message-ID: <20011016135210.16005.qmail@venus.postmark.net> Hi, I have some problems to set default program settings. I tried to put set emboss_verbose 1 in the emboss.default file but it doesn't seem to work. The command setenv emboss_verbose 1 doesn't work either, suggestions? From cutler at tularik.com Wed Oct 17 21:01:26 2001 From: cutler at tularik.com (Gene Cutler) Date: Wed, 17 Oct 2001 14:01:26 -0700 Subject: trouble indexing fasta database Message-ID: I am trying to index a fasta database and then retrieve sequences with seqret. I used dbifasta on half of the human genome golden path from ensembl: dbifasta -idformat simple -dbname ensembl_gp1 -directory . -filenames 'ensembl_golden_path.1' -indexdirectory /scratch1/databases/emboss/ and put this in my emboss.default: DB ensembl_gp1 [ type: N method: emblcd format: fasta dir: /scratch1/databases/raw/ file: ensembl_golden_path.1 indexdir: /scratch1/databases/emboss/ ] If I try to fetch a sequence located in the beginning of the fasta file, it works fine. But sequences further into the file aren't retrieved: > seqret ensembl_gp1:AC007798.1.15164.16328 Reads and writes (returns) sequences An error has been found: EMBLCD Entry failed An error has been found: Database 'ensembl_gp1' : access method 'emblcd' failed An error has been found: option -sequence: Unable to read sequence 'ensembl_gp1:AC007798.1.15164.16328' There is a serious problem: seqret terminated: Bad value for option and no prompt However, when I tried retrieving all the sequences: > seqret ensembl_gp1:* I got them all back. I can also retrieve the sequences if I get them directly from the fasta file rather than using the index. That makes it seem to be an index problem. Recreating the indexes hasn't helped. From mbehnke at vmbmod10.msu.montana.edu Wed Oct 17 22:39:40 2001 From: mbehnke at vmbmod10.msu.montana.edu (Michael Behnke) Date: Wed, 17 Oct 2001 16:39:40 -0600 (MDT) Subject: getorf Message-ID: I have been using the getorf program recently to find ORF's in Cryptosporidium contigs with great results. I do have a question though. Does anyone know what are the STOP and START codons used by the program, and do they change depending upon the table one uses? I see that plotorf uses Stop codons = TAA,TAG,TGA and Start codon = ATG, are these the same for getorf? Thanks Mike Behnke Bioinformatics Tech White Lab Montana State University From gwilliam at hgmp.mrc.ac.uk Thu Oct 18 12:40:55 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 18 Oct 2001 13:40:55 +0100 Subject: getorf References: Message-ID: <3BCECDD7.E9F070C1@hgmp.mrc.ac.uk> Michael Behnke wrote: > > I have been using the getorf program recently to find ORF's in > Cryptosporidium contigs with great results. I do have a question though. > Does anyone know what are the STOP and START codons used by the program, > and do they change depending upon the table one uses? I see that plotorf > uses Stop codons = TAA,TAG,TGA and Start codon = ATG, are these the same > for getorf? Yes, the STOP & START codons are held in the genetic code tables and will change with the table you choose. By default this is the Standard Code (See http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c) The STOP & START codons in the default table are, as you describe above, Stop codons = TAA,TAG,TGA and Start codon = ATG. The '-table' qualifier allows you to pick other tables. 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