From owner-srs@net.bio.net Sun Sep 03 23:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!newsfeed.internetmci.com!howland.reston.ans.net!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!news.vub.ac.be!usenet From: pinstall@sga.ulb.ac.be (Patrick Installe) Newsgroups: bionet.software.srs Subject: Parsing Date: Mon, 04 Sep 1995 15:16:46 GMT Organization: Université Libre de Bruxelles Lines: 40 Message-ID: <42f5d8$5hd@rc1.vub.ac.be> Reply-To: pinstall@sga.ulb.ac.be NNTP-Posting-Host: sga-pc6.ulb.ac.be. X-Newsreader: Forte Free Agent 1.0.82 Hello, I am evaluating the possibility to use SRS (wgetz) for a database in a genbank like format. As SRS already has (uses?) a parser ("Odd" currently and "Icarus" in the future) for the output, I would like to use the same parser to improve the input of data. I must say that I can't find my way. Basically I would like to get from an entry of the database : elements or a list(?tree?) of the element in such a way that a program can help in correcting the input by some validation. The ideal would be to be able to propose a previous entry as a template for the next one. Is there somebody who succeeded along such a path, any pointer, experience ? Since I have not find any reference (archie and www databases) to "Odd" and "Icarus". How far are these parser more or less deeply linked to SRS. Is it possible to get ASCII flat file as output ? Thank your very much in advance for your help. By the Way : I would appreciate to conserve the difference between upper an lower case. For example, it is the way the biologist make the distinction between a gene and its product ! `'~*-,._.,-*~'`^`'~*-,._.,-*~'`^`'~*-,._.,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ Patrick Installe pinstall@sga.ulb.ac.be Universite Libre de Bruxelles Secretariat Tel : +32-(0)67-88.94.61 Service de Genetique Appliquee +32-(0)2-650.94.61 Rue de l'industrie, 24 Fax : +32-(0)67-88.94.77 B-1400 Nivelles Email : genapp@sga.ulb.ac.be `'~*-,._.,-*~'`^`'~*-,._.,-*~'`^`'~*-,._.,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ From owner-srs@net.bio.net Mon Sep 04 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: Parsing Date: 5 Sep 1995 18:25:05 GMT Organization: EMBL Heidelberg Lines: 24 Distribution: world Message-ID: <42i4m1$mtv@lion.embl-heidelberg.de> References: <42f5d8$5hd@rc1.vub.ac.be> NNTP-Posting-Host: falcon.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX 5.3 IP20) X-URL: news:42f5d8$5hd@rc1.vub.ac.be pinstall@sga.ulb.ac.be (Patrick Installe) wrote: > Hello, > > I am evaluating the possibility to use SRS (wgetz) for a database >in a genbank like format. > > As SRS already has (uses?) a parser ("Odd" currently and "Icarus" >in the future) for the output, I would like to use the same parser to >improve the input of data. > > I must say that I can't find my way. Basically I would like to get > hi patrick, i don't recommend using the old parser outside of SRS. we are currently working on icarus ...it is mostly cleaning up code and do a few last things ....it will probably suitable for what you want to do. it will probably ~2months until ready for beta-testing and we will announce it in this newsgroup. Icarus can be used 'outside' of SRS. regards thure From owner-srs@net.bio.net Tue Sep 05 23:00:00 1995 Path: biosci!daresbury!usenet From: "M.P. Hilbers" Newsgroups: bionet.software.srs Subject: ANNOUNCEMENT: SRS-server at SEQNET Date: 6 Sep 1995 08:37:37 GMT Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 7 Distribution: bionet Message-ID: <42jmkh$k26@mserv1.dl.ac.uk> NNTP-Posting-Host: s-crim1.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.2 IP17) X-URL: news:bionet.software.srs A new SRS-server is now operational at SEQNET, allowing access to the usual collection of sequence databases and to a number of other biological databases available at SEQNET, the UK EMBNet node at Daresbury. It can be found at http://seqnet.dl.ac.uk/srs/srsc Martin Hilbers, SEQNET From owner-srs@net.bio.net Tue Sep 05 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: ANNOUNCEMENT: SRS-server at SEQNET Date: 6 Sep 1995 13:27:39 GMT Organization: EMBL Heidelberg Lines: 24 Distribution: world Message-ID: <42k7kb$5pm@lion.embl-heidelberg.de> References: <42jmkh$k26@mserv1.dl.ac.uk> NNTP-Posting-Host: falcon.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX 5.3 IP20) X-URL: news:42jmkh$k26@mserv1.dl.ac.uk "M.P. Hilbers" wrote: >A new SRS-server is now operational at SEQNET, allowing access to the usual >collection of sequence databases and to a number of other biological databases >available at SEQNET, the UK EMBNet node at Daresbury. >It can be found at http://seqnet.dl.ac.uk/srs/srsc > >Martin Hilbers, SEQNET > dear martin, ..i put you into the list for the 'status.html'! regards thure -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Tue Sep 05 23:00:00 1995 Path: biosci!student.umass.edu!stakbone From: stakbone@student.umass.edu (Michael A Wachala) Newsgroups: bionet.software.srs Subject: unsubscribe Date: 6 Sep 1995 09:38:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <199509061635.MAA07841@titan.oit.umass.edu> NNTP-Posting-Host: net.bio.net unsubscribe From owner-srs@net.bio.net Mon Sep 11 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software,bionet.software.srs Subject: SRS-FastA: Similarity searches of Genbank subsets Date: 12 Sep 1995 16:44:27 GMT Organization: Biology, Indiana University - Bloomington Lines: 41 Message-ID: <434ddb$llc@usenet.ucs.indiana.edu> NNTP-Posting-Host: sunflower.bio.indiana.edu Xref: biosci bionet.software:13293 bionet.software.srs:145 SRS-FASTA (or GenBank subset search) A new service is available to match your query sequence against subsets of nucleic and protein databanks. These subsets are chosen by you with keyword selections in the sequence documentation. There may be times when you will get better information by eliminating unwanted sections of the databanks before performing a sequence search. Given the large size and constant updates to the biosequence databanks, it is difficult to produce subsets of these data directly for similarity searching. By coupling similarity search software (FastA) with keyword selection software (SRS), one can provide such searches fairly efficiently. Find this service the Genbank-Sequences/ section at IUBio Archive (http://iubio.bio.indiana.edu/): Linkname: [text ] SRS-FASTA: Similarity Search of GenBank Subsets Filename: http://iubio.bio.indiana.edu:81/srsfasta This is an experimental service. It may be unavailable at times. It is running on a computer that is already frequently loaded with other processing jobs (the flybase and iubio services). Other biocomputing centers are most welcome to duplicate and improve on this service. Please contact Don Gilbert for help. Your feedback on this service is essential to improving it. Please send your suggestions and comments to software@bio.indiana.edu If I receive enough requests from people, I can make a gopher+ version of this available. Acknowledgements: This service is possible only due to the excellent FastA software of W.Pearson and colleages, and the excellent SRS software of Thure Etzold and collleages. I wish to thank Ugawa Yoshihiro, who brought to my attention the interest in such a service. -- Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Sun Sep 17 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!in2.uu.net!fonorola!news.citenet.net!G5-204 From: MTL@AMAV.COM (AMAV Industries) Newsgroups: bionet.software.srs Subject: Wanted: Educational Software!!!! Date: Mon, 18 Sep 95 19:04:11 GMT Organization: CiteNet Telecom - Commercial Internet Service Lines: 12 Message-ID: <43kg0a$su6@cti01.citenet.net> NNTP-Posting-Host: g5-204.citenet.net X-Newsreader: News Xpress Version 1.0 Beta #4 Hello, we are a leading toy distributor in Canada and are interested in distributing a line of educational software to our clients. As such, we are looking to buy the rights to various educational software products for cash or on a royalty basis. If you have anything that you think might be of interest to us, please contact us by phone: (514) 344-1234 by fax: (514) 344-1235 by e-mail: MTL@AMAV.COM (attn: Yehuda) Thank-you! From owner-srs@net.bio.net Thu Sep 21 23:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!usenet From: Tylzanowski Przemko Newsgroups: bionet.software.srs Subject: feature table Date: 22 Sep 1995 08:04:01 GMT Organization: Brussels Free Universities VUB/ULB Lines: 12 Message-ID: <43tqlh$pmv@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be. Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; OSF1 V3.2 alpha) X-URL: news:bionet.software.srs Hi! I would like to do "isolate" some specific features from genes in which I am interested. Now, the problem is that srs seems to recognize only the feature name not contents. Specifically, if I want to get only cytoplasmic domains of some proteins I do 'feature'-domain. Then I get a lot of entries, since there are other domains that cytoplasmic ones. If, on the other hand I put 'feature'- domain & cytoplasmic then I get nothing, presumably because the search strategy does not enter the description of the feature. Oh, boy, I hope it is clear. Anyone could help me? Przemko From owner-srs@net.bio.net Thu Sep 21 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: feature table Date: 22 Sep 1995 15:29:18 GMT Organization: EMBL Heidelberg Lines: 26 Distribution: world Message-ID: <43ukoe$gbl@lion.embl-heidelberg.de> References: <43tqlh$pmv@rc1.vub.ac.be> NNTP-Posting-Host: phenix.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX64 6.1 IP21) To: przemko X-URL: news:43tqlh$pmv@rc1.vub.ac.be Tylzanowski Przemko wrote: >I would like to do "isolate" some specific features from genes in which I am >interested. Now, the problem is that srs seems to recognize only the feature >name not contents. Specifically, if I want to get only cytoplasmic domains of >some proteins I do 'feature'-domain. Then I get a lot of entries, since there >are other domains that cytoplasmic ones. If, on the other hand I put 'feature'- >domain & cytoplasmic then I get nothing, presumably because the search strategy >does not enter the description of the feature. >Oh, boy, I hope it is clear. >Anyone could help me? not sure which databank you use ...works fine with SwissProt searched "cytoplasmic&domain" in the "features" field and got ~5000 subentries SRS puts the feature name AND the feature description into the index regards thure -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Thu Sep 21 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: feature table Date: 22 Sep 1995 15:29:30 GMT Organization: EMBL Heidelberg Lines: 26 Distribution: world Message-ID: <43ukoq$gbl@lion.embl-heidelberg.de> References: <43tqlh$pmv@rc1.vub.ac.be> NNTP-Posting-Host: phenix.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX64 6.1 IP21) X-URL: news:43tqlh$pmv@rc1.vub.ac.be Tylzanowski Przemko wrote: >I would like to do "isolate" some specific features from genes in which I am >interested. Now, the problem is that srs seems to recognize only the feature >name not contents. Specifically, if I want to get only cytoplasmic domains of >some proteins I do 'feature'-domain. Then I get a lot of entries, since there >are other domains that cytoplasmic ones. If, on the other hand I put 'feature'- >domain & cytoplasmic then I get nothing, presumably because the search strategy >does not enter the description of the feature. >Oh, boy, I hope it is clear. >Anyone could help me? not sure which databank you use ...works fine with SwissProt searched "cytoplasmic&domain" in the "features" field and got ~5000 subentries SRS puts the feature name AND the feature description into the index regards thure -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Tue Sep 26 23:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Retrieving features with SRS : the problem Date: 27 Sep 1995 10:44:01 GMT Organization: Belgian EMBnet Node Lines: 17 Message-ID: <44b9th$kdv@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be. X-Newsreader: TIN [version 1.2 PL2] SRS allows to retrieve parts of sequences corresponding to features mentioned in the documentation. However, it does not work entirely satisfactorily : - with the WWW interface : if you select "sequenceFeatures" in the pull-down menu of the QueryForm, SRS does generate separate entries for each feature, but it contains the complete sequence, not just the feature. - with the srscurses and the srstk interfaces : if the sequence contains several features of the same type, SRS retrieves files with the entries put the one behind the other (what makes that they cannot be taken as input by software as GCG). Anybody comments about this ? Dr. Guy Bottu From owner-srs@net.bio.net Tue Sep 26 23:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!usenet From: Tylzanowski Przemko Newsgroups: bionet.software.srs Subject: Re: Retrieving features with SRS : the problem Date: 27 Sep 1995 12:33:27 GMT Organization: Brussels Free Universities VUB/ULB Lines: 27 Message-ID: <44bgan$mld@rc1.vub.ac.be> References: <44b9th$kdv@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be. Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; OSF1 V3.2 alpha) X-URL: news:44b9th$kdv@rc1.vub.ac.be gbottu@ben.vub.ac.be (Guy Bottu) wrote: >SRS allows to retrieve parts of sequences corresponding to features >mentioned in the documentation. However, it does not work entirely >satisfactorily : > >- with the WWW interface : if you select "sequenceFeatures" in the > pull-down menu of the QueryForm, SRS does generate separate entries > for each feature, but it contains the complete sequence, not just the > feature. Not really, if you try to ask for "show-sequenceFeatures" instead of "entries"(default). Then you get only the sequence of the feature. It will happen if, after getting the list of hits you ask for "complete entries". If on the search page you have asked for SequenceFeature that you will get features only. >- with the srscurses and the srstk interfaces : if the sequence > contains several features of the same type, SRS retrieves files > with the entries put the one behind the other (what makes > that they cannot be taken as input by software as GCG). > I think that if you save it in the GCG format, you will get it the right way. I have encountered another problem here. I do the search, get a result, ask-List entries and I get a list. BUT, if I want to see antry I get an empty page. Also if I try to copy the set I get an empty file Przemko From owner-srs@net.bio.net Tue Sep 26 23:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Re: Retrieving features with SRS : the problem Date: 27 Sep 1995 15:48:25 GMT Organization: Belgian EMBnet Node Lines: 25 Message-ID: <44bro9$o8m@rc1.vub.ac.be> References: <44b9th$kdv@rc1.vub.ac.be> <44bgan$mld@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be. X-Newsreader: TIN [version 1.2 PL2] Tylzanowski Przemko (przemko) wrote: : Not really, if you try to ask for "show-sequenceFeatures" instead of : "entries"(default). Then you get only the sequence of the feature. It will : happen if, after getting the list of hits you ask for "complete entries". If on : the search page you have asked for SequenceFeature that you will get features : only. Not at all, you get the complete sequence. It is however possible to retrieve just the feature by clicking on the hyperlink. : I think that if you save it in the GCG format, you will get it the right way. Again, not at all : I have encountered another problem here. I do the search, get a result, ask-List : entries and I get a list. BUT, if I want to see antry I get an empty page. Also : if I try to copy the set I get an empty file I think this was a temporary problem that has nothing to do with the SRS software itself. At the BEN site, we have recently installed the new release of EMBL. Because of its size, it took a lot of time, and there was a period during which the databank and the SRS indexes were not at pace. Dr. Guy Bottu