From stefanielager at fastmail.ca Wed Dec 1 07:58:03 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Wed, 1 Dec 2004 12:58:03 +0000 (UTC) Subject: [EMBOSS] External DB problems Message-ID: <20041201125803.B6F4C8613EC@mail.interchange.ca> Hi, In version 2.8.0 of EMBOSS I have problems to access external databases (UniProt)using methods URL and SRSWWW. It's not a proxy problem since app: "wget http://www.ebi.ac.uk/cgi-bin/dbfetch?db=UniProt&id=%s" works nice. But I can't get DB uniprot [ type: P format: embl method: url url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[uniprot-AllText:%s]" ] or DB uniprot [ type: P format: embl method: srswww url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" ] to work. In both cases it trys for a very long time and then times out with the message: "Error: socket connect failed for database 'uniprot' socket connect failed for database 'uniprot': Connection timed out" Does anyone know what could be wrong? Stefanie _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From pmr at ebi.ac.uk Wed Dec 1 08:59:19 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 01 Dec 2004 13:59:19 +0000 Subject: [EMBOSS] External DB problems In-Reply-To: <20041201125803.B6F4C8613EC@mail.interchange.ca> References: <20041201125803.B6F4C8613EC@mail.interchange.ca> Message-ID: <41ADCE37.50608@ebi.ac.uk> Stefanie Lager wrote: > Hi, > > In version 2.8.0 of EMBOSS I have problems to access external databases > (UniProt)using methods URL and SRSWWW. It's not a proxy problem since > > app: "wget http://www.ebi.ac.uk/cgi-bin/dbfetch?db=UniProt&id=%s" > > works nice. > > But I can't get > > DB uniprot [ > type: P > format: embl > method: url > url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[uniprot-AllText:%s]" > ] > > or > > DB uniprot [ > type: P > format: embl > method: srswww > url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" > ] > > > to work. In both cases it trys for a very long time and then times out > with the message: > > "Error: socket connect failed for database 'uniprot' > socket connect failed for database 'uniprot': Connection timed out" > > Does anyone know what could be wrong? Firstly, it could still be a proxy problem. Your wget application will not use an EMBOSS proxy definition which should be defined as EMBOSS_PROXY as an environment variable, or in emboss.default (or your own ~/.embossrc) as something like: SET emboss_proxy "proxy.mydomain.ac.uk:8080" UniProt in SRS is running a little slowly but should work for you. You shuold however define it as: url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[uniprot-AllText:%s]+-ascii" (otherwise you will be trting to read HTML output from SRS). The SRSWWW definition is fine .. well, it works for me. Hope this helps, let me know if it's not a proxy problem. Peter Rice From golharam at umdnj.edu Thu Dec 2 16:22:57 2004 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 02 Dec 2004 16:22:57 -0500 Subject: [EMBOSS] EMBOSS Web Interface Message-ID: <000901c4d8b5$17a33a70$a6028a0a@GOLHARMOBILE1> Hi all, I'm looking for a simple web interface to EMBOSS. I liked EMBOSS::GUI, but development on it seems to have stopped and I'm running into some problems with it and not sure who to ask. wEMBOSS feels a lot like SeqWeb and its much more than we want. Can anyone recommend a good, simple web interface to EMBOSS? ----- Ryan Golhar Computational Biologist The Informatics Institute at The University of Medicine & Dentistry of NJ Phone: 973-972-5034 Fax: 973-972-7412 Email: golharam at umdnj.edu From ashgene at yahoo.co.in Thu Dec 2 19:14:00 2004 From: ashgene at yahoo.co.in (Ahamarshan jn) Date: Thu, 2 Dec 2004 16:14:00 -0800 (PST) Subject: [EMBOSS] how to convert gcg file format to emboss file format Message-ID: <20041203001400.96570.qmail@web8507.mail.in.yahoo.com> Hi i want to convert the .codon file format to .cut file format of EMBOSS - ash --------------------------------- Do you Yahoo!? Send a seasonal email greeting and help others. Do good. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20041202/3045ca3c/attachment.html From lukem at gene.pbi.nrc.ca Thu Dec 2 19:23:23 2004 From: lukem at gene.pbi.nrc.ca (Luke McCarthy) Date: Thu, 02 Dec 2004 18:23:23 -0600 Subject: [EMBOSS] EMBOSS Web Interface In-Reply-To: <000901c4d8b5$17a33a70$a6028a0a@GOLHARMOBILE1> References: <000901c4d8b5$17a33a70$a6028a0a@GOLHARMOBILE1> Message-ID: <1102033403.8501.14.camel@kerouac.private.virtuouspagans.org> On Thu, 2004-12-02 at 15:22, Ryan Golhar wrote: > Hi all, > > I'm looking for a simple web interface to EMBOSS. I liked > EMBOSS::GUI, but development on it seems to have stopped and > I'm running into some problems with it and not sure who to ask. Hi Ryan, Development on EMBOSS::GUI had indeed stopped, but resumed last week ;) I expect a new release very, very soon. Hopefully next week. I've set up a project on SourceForge to host development (http://embossgui.sourceforge.net). There's nothing there right now, but stay tuned. I'll post a followup message to this list when there's something to see there. Cheers, Luke From pmr at ebi.ac.uk Fri Dec 3 04:12:48 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 03 Dec 2004 09:12:48 +0000 Subject: [EMBOSS] EMBOSS Web Interface Message-ID: <41B02E10.5090006@ebi.ac.uk> Ryan Golhar wrote: > Hi all, > > I'm looking for a simple web interface to EMBOSS. I liked EMBOSS::GUI, > but development on it seems to have stopped and I'm running into some > problems with it and not sure who to ask. > > wEMBOSS feels a lot like SeqWeb and its much more than we want. Can > anyone recommend a good, simple web interface to EMBOSS? I am planning to survey all the EMBOSS interfaces. My problem is finding them. If anyone knows of an interface not listed on our current web page http://emboss.sourceforge.net/interfaces/ please tell me more about it and I will include it in the survey. regards, Peter Rice From golharam at umdnj.edu Fri Dec 3 09:39:46 2004 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 3 Dec 2004 09:39:46 -0500 Subject: [EMBOSS] EMBOSS Web Interface In-Reply-To: <1102032966.8501.11.camel@kerouac.private.virtuouspagans.org> Message-ID: <003901c4d945$efe8aab0$a6028a0a@GOLHARMOBILE1> Hey Luke, That's great news. EMBOSS::GUI is the only simple web interface I could find, and that my users like. If you'd like any help on development of it, pleae let me know, I'd be more than happy to help if I can. Ryan -----Original Message----- From: Luke McCarthy [mailto:lukem at gene.pbi.nrc.ca] Sent: Thursday, December 02, 2004 7:16 PM To: emboss at embnet.org Cc: golharam at umdnj.edu Subject: Re: [EMBOSS] EMBOSS Web Interface On Thu, 2004-12-02 at 15:22, Ryan Golhar wrote: > Hi all, > > I'm looking for a simple web interface to EMBOSS. I liked > EMBOSS::GUI, but development on it seems to have stopped and I'm > running into some problems with it and not sure who to ask. Hi Ryan, Development on EMBOSS::GUI had indeed stopped, but resumed last week ;) I expect a new release very, very soon. Hopefully next week. I've set up a project on SourceForge to host development (http://embossgui.sourceforge.net). There's nothing there right now, but stay tuned. I'll post a followup message to this list when there's something to see there. Cheers, Luke From stefanielager at fastmail.ca Tue Dec 7 08:08:20 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Tue, 7 Dec 2004 13:08:20 +0000 (UTC) Subject: [EMBOSS] Fetching PDB entries Message-ID: <20041207130821.281B48614F9@mail.interchange.ca> Hi, Is there a way to fetch single PDB entries externally with EMBOSS yet? Are there other any other scripts to fetch single PDB entries externally? Stefanie _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From jison at hgmp.mrc.ac.uk Tue Dec 7 08:24:31 2004 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Tue, 07 Dec 2004 13:24:31 +0000 Subject: [EMBOSS] Fetching PDB entries References: <20041207130821.281B48614F9@mail.interchange.ca> Message-ID: <41B5AF0F.C04C6B08@hgmp.mrc.ac.uk> Hi Stefanie The short answer is "not at the moment but hopefully for the next (2005) release". All the underlying code for correctly parsing the PDB format is there but this isn't yet reflected in ACD file handling and the command line. I'm planning on the equivalent of a USA (uniform sequence address) for structures, which would support all retrieval modes, e.g. over web, and a "structure" ACD type. Beyond that it depends what you wanted to do with the PDB file. The above applies to SCOP & CATH too. Please let me know what you need and I'll try and accommodate ... Cheers Jon Stefanie Lager wrote: > > Hi, > > Is there a way to fetch single PDB entries externally with EMBOSS yet? > Are there other any other scripts to fetch single PDB entries externally? > > Stefanie > _________________________________________________________________ > http://fastmail.ca/ - Fast Secure Web Email for Canadians -- Jon C. Ison, PhD Proteomics Applications Group MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494500 Fax: +44 1223 494512 E-mail: jison at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk From sbassi at gmail.com Tue Dec 7 08:27:01 2004 From: sbassi at gmail.com (Sebastian Bassi) Date: Tue, 7 Dec 2004 10:27:01 -0300 Subject: [EMBOSS] Fetching PDB entries In-Reply-To: <20041207130821.281B48614F9@mail.interchange.ca> References: <20041207130821.281B48614F9@mail.interchange.ca> Message-ID: On Tue, 7 Dec 2004 13:08:20 +0000 (UTC), Stefanie Lager wrote: > Hi, > Is there a way to fetch single PDB entries externally with EMBOSS yet? > Are there other any other scripts to fetch single PDB entries externally? BioPython have a PDB parser. It is not EMBOSS but may help you. From yezq at mail.cbi.pku.edu.cn Mon Dec 20 01:56:08 2004 From: yezq at mail.cbi.pku.edu.cn (Zhiqiang Ye) Date: Mon, 20 Dec 2004 14:56:08 +0800 Subject: [EMBOSS] Is srswww related to srs version? Message-ID: <200412200656.iBK6uSi2016693@mail.cbi.pku.edu.cn> Dear all?? ????I encountered a problem about "seqret" program to get some sequences using "srswww". My ~/.embossrc file is like this: # swall sequence from cbi srs server DB swcbi [ type: P method: srswww format: swiss dbalias: swissprot url: "http://srs.pku.edu.cn/srs7bin/cgi-bin/wgetz" comment: "Swissprot and Trembl from CBI SRS Server" ] # uniprot sequence from ebi srs server DB swebi [ type: P method: srswww format: swiss dbalias: swissprot url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" comment: "swissprot from EBI SRS Server" ] The command I used for getting sequences: %> seqret swcbi:aroa_* This will get only 30 sequences from srs.pku.edu.cn But if I use the srs through web exlorer, use "aroa_" to search the ID of swissprot, I can get 104 sequences whose id is like "aroa_*". %> seqret swebi:aroa_* This will get 105 sequences from srs.ebi.ac.uk This is the same as the results from web explorer. My embossversion is 2.9.0, the same problem occurs on another machine with emboss 2.6.0 I have no idea about this. Maybe it is the different SRS version or the different configuration between srs.pku.edu.cn and srs.ebi.ac.uk? Thank you. ???????????????? ????????????????????????????Zhiqiang Ye ??????????????????????????????????2004-12-20 ############################################################### Zhiqiang Ye, Ph. D candidate, Major in Bioinformatics Center of BioInformatics, College of Life Scicences, Peking University, Beijing, PR China 100871 ############################################################### From stefanielager at fastmail.ca Wed Dec 1 12:58:03 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Wed, 1 Dec 2004 12:58:03 +0000 (UTC) Subject: [EMBOSS] External DB problems Message-ID: <20041201125803.B6F4C8613EC@mail.interchange.ca> Hi, In version 2.8.0 of EMBOSS I have problems to access external databases (UniProt)using methods URL and SRSWWW. It's not a proxy problem since app: "wget http://www.ebi.ac.uk/cgi-bin/dbfetch?db=UniProt&id=%s" works nice. But I can't get DB uniprot [ type: P format: embl method: url url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[uniprot-AllText:%s]" ] or DB uniprot [ type: P format: embl method: srswww url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" ] to work. In both cases it trys for a very long time and then times out with the message: "Error: socket connect failed for database 'uniprot' socket connect failed for database 'uniprot': Connection timed out" Does anyone know what could be wrong? Stefanie _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From pmr at ebi.ac.uk Wed Dec 1 13:59:19 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 01 Dec 2004 13:59:19 +0000 Subject: [EMBOSS] External DB problems In-Reply-To: <20041201125803.B6F4C8613EC@mail.interchange.ca> References: <20041201125803.B6F4C8613EC@mail.interchange.ca> Message-ID: <41ADCE37.50608@ebi.ac.uk> Stefanie Lager wrote: > Hi, > > In version 2.8.0 of EMBOSS I have problems to access external databases > (UniProt)using methods URL and SRSWWW. It's not a proxy problem since > > app: "wget http://www.ebi.ac.uk/cgi-bin/dbfetch?db=UniProt&id=%s" > > works nice. > > But I can't get > > DB uniprot [ > type: P > format: embl > method: url > url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[uniprot-AllText:%s]" > ] > > or > > DB uniprot [ > type: P > format: embl > method: srswww > url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" > ] > > > to work. In both cases it trys for a very long time and then times out > with the message: > > "Error: socket connect failed for database 'uniprot' > socket connect failed for database 'uniprot': Connection timed out" > > Does anyone know what could be wrong? Firstly, it could still be a proxy problem. Your wget application will not use an EMBOSS proxy definition which should be defined as EMBOSS_PROXY as an environment variable, or in emboss.default (or your own ~/.embossrc) as something like: SET emboss_proxy "proxy.mydomain.ac.uk:8080" UniProt in SRS is running a little slowly but should work for you. You shuold however define it as: url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[uniprot-AllText:%s]+-ascii" (otherwise you will be trting to read HTML output from SRS). The SRSWWW definition is fine .. well, it works for me. Hope this helps, let me know if it's not a proxy problem. Peter Rice From golharam at umdnj.edu Thu Dec 2 21:22:57 2004 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 02 Dec 2004 16:22:57 -0500 Subject: [EMBOSS] EMBOSS Web Interface Message-ID: <000901c4d8b5$17a33a70$a6028a0a@GOLHARMOBILE1> Hi all, I'm looking for a simple web interface to EMBOSS. I liked EMBOSS::GUI, but development on it seems to have stopped and I'm running into some problems with it and not sure who to ask. wEMBOSS feels a lot like SeqWeb and its much more than we want. Can anyone recommend a good, simple web interface to EMBOSS? ----- Ryan Golhar Computational Biologist The Informatics Institute at The University of Medicine & Dentistry of NJ Phone: 973-972-5034 Fax: 973-972-7412 Email: golharam at umdnj.edu From ashgene at yahoo.co.in Fri Dec 3 00:14:00 2004 From: ashgene at yahoo.co.in (Ahamarshan jn) Date: Thu, 2 Dec 2004 16:14:00 -0800 (PST) Subject: [EMBOSS] how to convert gcg file format to emboss file format Message-ID: <20041203001400.96570.qmail@web8507.mail.in.yahoo.com> Hi i want to convert the .codon file format to .cut file format of EMBOSS - ash --------------------------------- Do you Yahoo!? Send a seasonal email greeting and help others. Do good. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lukem at gene.pbi.nrc.ca Fri Dec 3 00:23:23 2004 From: lukem at gene.pbi.nrc.ca (Luke McCarthy) Date: Thu, 02 Dec 2004 18:23:23 -0600 Subject: [EMBOSS] EMBOSS Web Interface In-Reply-To: <000901c4d8b5$17a33a70$a6028a0a@GOLHARMOBILE1> References: <000901c4d8b5$17a33a70$a6028a0a@GOLHARMOBILE1> Message-ID: <1102033403.8501.14.camel@kerouac.private.virtuouspagans.org> On Thu, 2004-12-02 at 15:22, Ryan Golhar wrote: > Hi all, > > I'm looking for a simple web interface to EMBOSS. I liked > EMBOSS::GUI, but development on it seems to have stopped and > I'm running into some problems with it and not sure who to ask. Hi Ryan, Development on EMBOSS::GUI had indeed stopped, but resumed last week ;) I expect a new release very, very soon. Hopefully next week. I've set up a project on SourceForge to host development (http://embossgui.sourceforge.net). There's nothing there right now, but stay tuned. I'll post a followup message to this list when there's something to see there. Cheers, Luke From pmr at ebi.ac.uk Fri Dec 3 09:12:48 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 03 Dec 2004 09:12:48 +0000 Subject: [EMBOSS] EMBOSS Web Interface Message-ID: <41B02E10.5090006@ebi.ac.uk> Ryan Golhar wrote: > Hi all, > > I'm looking for a simple web interface to EMBOSS. I liked EMBOSS::GUI, > but development on it seems to have stopped and I'm running into some > problems with it and not sure who to ask. > > wEMBOSS feels a lot like SeqWeb and its much more than we want. Can > anyone recommend a good, simple web interface to EMBOSS? I am planning to survey all the EMBOSS interfaces. My problem is finding them. If anyone knows of an interface not listed on our current web page http://emboss.sourceforge.net/interfaces/ please tell me more about it and I will include it in the survey. regards, Peter Rice From golharam at umdnj.edu Fri Dec 3 14:39:46 2004 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 3 Dec 2004 09:39:46 -0500 Subject: [EMBOSS] EMBOSS Web Interface In-Reply-To: <1102032966.8501.11.camel@kerouac.private.virtuouspagans.org> Message-ID: <003901c4d945$efe8aab0$a6028a0a@GOLHARMOBILE1> Hey Luke, That's great news. EMBOSS::GUI is the only simple web interface I could find, and that my users like. If you'd like any help on development of it, pleae let me know, I'd be more than happy to help if I can. Ryan -----Original Message----- From: Luke McCarthy [mailto:lukem at gene.pbi.nrc.ca] Sent: Thursday, December 02, 2004 7:16 PM To: emboss at embnet.org Cc: golharam at umdnj.edu Subject: Re: [EMBOSS] EMBOSS Web Interface On Thu, 2004-12-02 at 15:22, Ryan Golhar wrote: > Hi all, > > I'm looking for a simple web interface to EMBOSS. I liked > EMBOSS::GUI, but development on it seems to have stopped and I'm > running into some problems with it and not sure who to ask. Hi Ryan, Development on EMBOSS::GUI had indeed stopped, but resumed last week ;) I expect a new release very, very soon. Hopefully next week. I've set up a project on SourceForge to host development (http://embossgui.sourceforge.net). There's nothing there right now, but stay tuned. I'll post a followup message to this list when there's something to see there. Cheers, Luke From stefanielager at fastmail.ca Tue Dec 7 13:08:20 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Tue, 7 Dec 2004 13:08:20 +0000 (UTC) Subject: [EMBOSS] Fetching PDB entries Message-ID: <20041207130821.281B48614F9@mail.interchange.ca> Hi, Is there a way to fetch single PDB entries externally with EMBOSS yet? Are there other any other scripts to fetch single PDB entries externally? Stefanie _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From jison at hgmp.mrc.ac.uk Tue Dec 7 13:24:31 2004 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Tue, 07 Dec 2004 13:24:31 +0000 Subject: [EMBOSS] Fetching PDB entries References: <20041207130821.281B48614F9@mail.interchange.ca> Message-ID: <41B5AF0F.C04C6B08@hgmp.mrc.ac.uk> Hi Stefanie The short answer is "not at the moment but hopefully for the next (2005) release". All the underlying code for correctly parsing the PDB format is there but this isn't yet reflected in ACD file handling and the command line. I'm planning on the equivalent of a USA (uniform sequence address) for structures, which would support all retrieval modes, e.g. over web, and a "structure" ACD type. Beyond that it depends what you wanted to do with the PDB file. The above applies to SCOP & CATH too. Please let me know what you need and I'll try and accommodate ... Cheers Jon Stefanie Lager wrote: > > Hi, > > Is there a way to fetch single PDB entries externally with EMBOSS yet? > Are there other any other scripts to fetch single PDB entries externally? > > Stefanie > _________________________________________________________________ > http://fastmail.ca/ - Fast Secure Web Email for Canadians -- Jon C. Ison, PhD Proteomics Applications Group MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494500 Fax: +44 1223 494512 E-mail: jison at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk From sbassi at gmail.com Tue Dec 7 13:27:01 2004 From: sbassi at gmail.com (Sebastian Bassi) Date: Tue, 7 Dec 2004 10:27:01 -0300 Subject: [EMBOSS] Fetching PDB entries In-Reply-To: <20041207130821.281B48614F9@mail.interchange.ca> References: <20041207130821.281B48614F9@mail.interchange.ca> Message-ID: On Tue, 7 Dec 2004 13:08:20 +0000 (UTC), Stefanie Lager wrote: > Hi, > Is there a way to fetch single PDB entries externally with EMBOSS yet? > Are there other any other scripts to fetch single PDB entries externally? BioPython have a PDB parser. It is not EMBOSS but may help you. From yezq at mail.cbi.pku.edu.cn Mon Dec 20 06:56:08 2004 From: yezq at mail.cbi.pku.edu.cn (Zhiqiang Ye) Date: Mon, 20 Dec 2004 14:56:08 +0800 Subject: [EMBOSS] Is srswww related to srs version? Message-ID: <200412200656.iBK6uSi2016693@mail.cbi.pku.edu.cn> Dear all? ??I encountered a problem about "seqret" program to get some sequences using "srswww". My ~/.embossrc file is like this: # swall sequence from cbi srs server DB swcbi [ type: P method: srswww format: swiss dbalias: swissprot url: "http://srs.pku.edu.cn/srs7bin/cgi-bin/wgetz" comment: "Swissprot and Trembl from CBI SRS Server" ] # uniprot sequence from ebi srs server DB swebi [ type: P method: srswww format: swiss dbalias: swissprot url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz" comment: "swissprot from EBI SRS Server" ] The command I used for getting sequences: %> seqret swcbi:aroa_* This will get only 30 sequences from srs.pku.edu.cn But if I use the srs through web exlorer, use "aroa_" to search the ID of swissprot, I can get 104 sequences whose id is like "aroa_*". %> seqret swebi:aroa_* This will get 105 sequences from srs.ebi.ac.uk This is the same as the results from web explorer. My embossversion is 2.9.0, the same problem occurs on another machine with emboss 2.6.0 I have no idea about this. Maybe it is the different SRS version or the different configuration between srs.pku.edu.cn and srs.ebi.ac.uk? Thank you. ???????? ??????????????Zhiqiang Ye ?????????????????2004-12-20 ############################################################### Zhiqiang Ye, Ph. D candidate, Major in Bioinformatics Center of BioInformatics, College of Life Scicences, Peking University, Beijing, PR China 100871 ###############################################################