From owner-srs@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!rutgers!gatech!EU.net!Ireland.EU.net!maths.tcd.ie!web3.tcd.ie!gen035.gen.tcd.ie!user From: atlloyd@acer.gen.tcd.ie (Andrew T. Lloyd) Newsgroups: bionet.software.srs Subject: Swissprot to EMBL link ? Date: Wed, 05 Feb 1997 14:48:43 +0000 Organization: INCBI, Trinity College, Dublin 2, Ireland. Lines: 14 Message-ID: NNTP-Posting-Host: gen035.gen.tcd.ie SRS 4.08 question, Can someone tell me what .sdl to change so that the link from SwissProt to EMBL points at the Accession Number rather than the gi number ? I am wildly guessing it might be: c=@FETCH_NUCACCNO somewhere in hyperlink.sdl. Thanks for your help mummy/daddy. Andrew -- Andrew T. Lloyd Irish National Centre for BioInformatics INCBI atlloyd@acer.gen.tcd.ie http://acer.gen.tcd.ie Tel: (+353)-1-608-1969 EMBnet Ireland Fax: (+353)-679-8558 From owner-srs@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: Swissprot to EMBL link ? Date: 06 Feb 1997 11:09:28 GMT Organization: The Sanger Centre Lines: 51 Message-ID: References: NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: atlloyd@acer.gen.tcd.ie's message of Wed, 05 Feb 1997 14:48:43 +0000 In article atlloyd@acer.gen.tcd.ie (Andrew T. Lloyd) writes: > SRS 4.08 question, > > Can someone tell me what .sdl to change so that the link from > SwissProt to EMBL points at the Accession Number rather than > the gi number ? I am wildly guessing it might be: > c=@FETCH_NUCACCNO somewhere in hyperlink.sdl. Thanks for your > help mummy/daddy. You can pick up (almost) any site's SDL files through their database help pages (the exceptions are new databases where the /oddfile="dbname.sdl" bit was left out accidentally). For example, http://www.embl-heidelberg.de/srs/srsc?-info+swissprot Pick up Thure's swissprot.sdl and hyperlink.sdl files (at the bottom of the page) and use diff to find the changes. Most differences in hyperlink.sdl will be for other databases (this is so much cleaner in SRS 5 :-) but you should easily find the line(s) you need. Comparing mine to yours (swissprot.sdl that is, best saved as text from netscape) : swissprot.sdl looks fine. hyperlink.sdl needs one small change (I lost a few spaces to make it fit better in this posting). dublin> emblref = 'EMBL;' ~A-Z0-9~ ';' ~A-Z0-9~ ; sanger> emblref = 'EMBL;' ~A-Z0-9~ ; So you are looking at the second "Xnnnnnn" text, and using it as an EMBL ID (which it isn't). Sanger looks at the first "Xnnnnn" text, and uses it as an EMBL accession number. That should be all you need. Change it, srssection to update the definitions, and browse away. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division, E-mail: pmr@sanger.ac.uk | The Sanger Centre, Tel: (44) 1223 494967 | Wellcome Trust Genome Campus, Fax: (44) 1223 494919 | Hinxton, Cambridge, CB10 1SA, URL: http://www.sanger.ac.uk/~pmr/ | England From owner-srs@net.bio.net Thu Feb 13 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news.maxwell.syr.edu!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!news.idt.net!nntp.farm.idt.net!ppp-22.ts-8.hck.idt.net!user From: myersm@rockvax.rockefeller.edu (Michael Myers) Newsgroups: bionet.software.srs Subject: grep searching Date: Fri, 14 Feb 1997 00:21:30 -0500 Organization: The Rockefeller University Lines: 64 Message-ID: NNTP-Posting-Host: ppp-22.ts-8.hck.idt.net I have been experimenting with the different SRS servers, most recently SRS 5 at Heidelberg. First, let me say it is wonderful service. The new View Manager is amazing. Now if I could just get to the point where I could save some results! Here are my questions (SRS 5 at EMBL unless otherwise mentioned). Is it allowable to connect grep expressions with boolean operators? for a single indice (eg. AllText): /^expression1$/ | /^expression2 $/ Since the manual says that all entries get converted to regular expressions anyway, I thought this would work. I never get data back, so I'm not sure if I'm trying to do something illegal or if the software isn't working properly. Here is a simple example to show some of the other troubles I'm having. I tried this expression and it returned a regex error (note that there is a space prior to the hyphen in the character set): In order to match "T cell" or "T-cell" /^t[ -]cell$/ (I discovered that the above expression does work from the EBI SRS server) The following just uses wildcards, but it fails to return any matches when I know that it should. t?lymphocyte | t?cell If I just search for "lymphocyte", I get some records which contain "T-lymphocyte" or "T-cell". I can't figure out why so many of my search terms fail. I also tried /^t.cell$/ from the EBI server and it worked fine. However, when I tried to join two searches (described below) from the Query Manager page, I got another error. Given the following searches: Q6 (retrieval) := "[Sequence-AllText:/^t[- ]cell$/] | [Sequence-AllText:/^t[- ]lymphocyte$/] | [Sequence-AllText:thymocyte]" found 303 entries 303 entries from SWISSPROT Q7 (retrieval) := "[Sequence-Organism:human]" found 4000 entries 4000 entries from SWISSPROT q6 & q7 returns the error: syntax error, at "cell$/] | [Sequence-AllText:/^t[- ]lymphocyte$/] | [Sequence-AllText:thymocyte]" Thanks for any clarification, Mike Myers Michael Myers Laboratory of Genetics The Rockefeller University 212-327-8233 (-7420 fax) myersm@rockvax.rockefeller.edu From owner-srs@net.bio.net Thu Feb 13 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!rill.news.pipex.net!pipex!warwick!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: grep searching Date: Fri, 14 Feb 1997 19:23:52 +0100 Organization: MRC Human Genome Resource Centre Lines: 22 Message-ID: <3304ADB8.7900@ebi.ac.uk> References: NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Sender: Thure Etzold X-Mailer: Mozilla 4.0b1 (Win95; I) To: Michael Myers X-Priority: Normal Michael Myers wrote: > > > Is it allowable to connect grep expressions with boolean operators? > > for a single indice (eg. AllText): /^expression1$/ | /^expression2 $/ > > Since the manual says that all entries get converted to regular > expressions anyway, I thought this would work. I never get data back, so > I'm not sure if I'm trying to do something illegal or if the software > isn't working properly. oops, yes you are right - the regular expressions work like this in srs4 and can be combined by boolean operators but i simply forgot to implement this in srs5 - which i will do now and make available in version 5.03. I will use all your examples and make sure they work regards thure From owner-srs@net.bio.net Fri Feb 14 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!metro.atlanta.com!uunet!in3.uu.net!194.179.1.100!minerva.ibernet.es!diana.ibernet.es!not-for-mail From: Enrique Tomás Newsgroups: bionet.software.srs Subject: Aedes Date: Sat, 15 Feb 1997 19:49:44 +0100 Organization: Unisource Espana NEWS SERVER Lines: 7 Message-ID: <33060548.7EB2@tsc.es> NNTP-Posting-Host: 194.224.193.193 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win95; I) Hi I am a Spanish biologist and could see something about "Chemical Attratcant Factor for Oviposition Traps for Females of the Genus Aedes"; the notice addressed to "http://gene.dbbm.fiocruz.br/biotech/bio3.html", but I can't find that URL. Can anybody help me? Many thanks. From owner-srs@net.bio.net Tue Feb 18 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Feb 1997 02:00:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199702191000.CAA03832@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-srs@net.bio.net Wed Feb 19 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!cs.utexas.edu!swrinde!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!uunet!in1.uu.net!192.174.65.41!01-newsfeed.univie.ac.at!02-newsfeed.univie.ac.at!news.via.at!caliope.ins.at!news From: "Postmaster@computer.at" Newsgroups: bionet.software.srs Subject: NEU! Das Service am Netz. Date: Thu, 20 Feb 1997 00:00:00 +0100 Organization: INS Kunden Lines: 28 Message-ID: <32F71DAE.6358@computer.at> NNTP-Posting-Host: cs02-16.ins.at Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) NEU ! Computer.at Internetservice Sie haben einen Computer? Keine Frage, Sie werden diesen Text ja kaum im Fernsehen lesen. Dann sollten Sie uns einmal besuchen: · Alle wichtigen Hersteller auf einen Blick, mit Links zu deren Seiten versteht sich! · Produktindex: Sie wollen ein Modem haben, wir sagen Ihnen wer’s baut, und was die Dinger können, mit Links zu den aktuellen Produktinfoseiten. · Vergleichstabellen für die wichtigsten Produkte, das haben sonst nur Händler! · Neuheiten am Markt, eine Übersicht, damit Sie heute nicht kaufen, was schon gestern ein Ladenhüter war. · Support durch Hardware-Profis, Sie liefern Ihr Problem, wir die Lösung. · Berichte über Interessantes am EDV-Markt. · Liste aller erfaßten Händler mit Produktspektrum, Öffnungszeiten, Telefon & Faxnummer,... Besuchen Sie uns: http://www.computer.at Das bringt’s ! From owner-srs@net.bio.net Wed Feb 19 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!news-peer.gsl.net!news.gsl.net!news.maxwell.syr.edu!news.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: Re: fasta and blast searches Date: 20 Feb 1997 13:00:58 GMT Organization: EMBL Heidelberg Lines: 33 Distribution: world Message-ID: <5ehhua$bri@lion.embl-heidelberg.de> References: <1997Feb20.130148@wehi> NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) X-URL: news:1997Feb20.130148@wehi janice@wehi.edu.au (Janice Coventry, Walter and Eliza Hall Institute) wrote: >Hello, > >Can anyone help me with blast and fasta searches? Do the blast and fasta >sources come with srs No.. upto my knowledge or do you have to have the programs running on the >machine srs is running on? Not necessarily, you can do you rsh to any other machine which can run these searches... check srswww.i which has 'rsh ' under launch label. >Also to set up the searches do you just have to uncomment the relevant parts of >srsdb.i and run srssection? whenever you modify srsdb.i you should do a srssection. Hope this helps, Thure might give more information. ramu =============================================================== Chenna Ramu | EMBL E-mail: chenna@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 356229 (Res) | 69012 Heidelberg (49) 6221 387398 (Off) | Germany Fax: (49) 6221 387517 URL: http://www.embl-heidelberg.de/~chenna/ =============================================================== From owner-srs@net.bio.net Wed Feb 19 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.unimelb.EDU.AU!wehi.edu.au!wehi!janice From: janice@wehi.edu.au (Janice Coventry, Walter and Eliza Hall Institute) Newsgroups: bionet.software.srs Subject: fasta and blast searches Date: 20 Feb 97 13:01:48 +1000 Organization: Walter & Eliza Hall Institute Lines: 12 Message-ID: <1997Feb20.130148@wehi> NNTP-Posting-Host: wehiw.wehi.edu.au Hello, Can anyone help me with blast and fasta searches? Do the blast and fasta sources come with srs or do you have to have the programs running on the machine srs is running on? Also to set up the searches do you just have to uncomment the relevant parts of srsdb.i and run srssection? Thanks, Janice From owner-srs@net.bio.net Wed Feb 19 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!cs.utexas.edu!howland.erols.net!cam-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.sprintlink.net!news-peer.sprintlink.net!rill.news.pipex.net!pipex!warwick!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: fasta and blast searches Date: Thu, 20 Feb 1997 17:09:36 +0100 Organization: MRC Human Genome Resource Centre Lines: 30 Message-ID: <330C7740.29EF@ebi.ac.uk> References: <1997Feb20.130148@wehi> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Sender: Thure Etzold X-Mailer: Mozilla 4.0b1 (Win95; I) X-Priority: Normal Janice Coventry, Walter and Eliza Hall Institute wrote: > > Hello, > > Can anyone help me with blast and fasta searches? Do the blast and fasta > sources come with srs or do you have to have the programs running on the > machine srs is running on? The SRS release does not contain any of these application programs but the next release 5.03 will support BLAST, FASTA and the Smith and Waterman search with the Bioccelerator. Also it supports Clustalw for multiple sequence alignment. The applications can be started on machines other than the one hosting the SRSWWW server through rshells. It is also possible to customize and add more search tools. I am currently writing documentation on how to do that. The integration with application programs is still at an exp. stage and the goal is to allow integration of many more programs. > Also to set up the searches do you just have to uncomment the relevant parts of > srsdb.i and run srssection? it will be something like that - but most likely some customization will have to be done - such as the path to the blast and fasta databanks regards thure > > Thanks, > Janice From owner-srs@net.bio.net Wed Feb 19 22:00:00 1997 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!news From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Re: fasta and blast searches Date: 20 Feb 1997 23:54:09 GMT Organization: Biology, Indiana University - Bloomington Lines: 216 Message-ID: <5eio71$cff@dismay.ucs.indiana.edu> References: <1997Feb20.130148@wehi> <330C7740.29EF@ebi.ac.uk> NNTP-Posting-Host: chipmunk.bio.indiana.edu Thure, I customized version 4 of SRS to produce a file of indices into databanks as a search result, and feed that into FastA (which was also customized) to allow one to do fasta searches w/o having to generate a temp data file that was huge. Is that of any interest to you or others (the srs customization)? I don't think I would want to run an SRS-fasta search that allowed users to generate temp files in the multi-gigabyte range, and even if I had that disk space, it would likely be slower than generating byte indices. -- Don The main function I had to add to srs4 was to list file indices, in the seqlib.c file, i added the SlbListFSE function below, then added an item to getz.c to allow calling it, plus a few configuration items (in the odd files). I haven't had a chance to port this to srs 5 yet, however I will do so when time permits. see http://iubio.bio.indiana.edu/srsfasta/ /* --- ListFSE parts --------------*/ /* dgg - from hash.c, for hashing file names... */ static long HashString(void *s) { register unsigned long h=0, g; register char *p = (char *) s; while (*p) { h= (h << 4) + *p++; if ((g= (h & 0xf0000000))) h= (h ^ (g >> 24)) ^ g; } return (long) h; } static long lastdocstart = -1; static short lastfileid = -1; static long nFofn = 0, maxFofn = 0; static long * hashFofn = NULL; char * gOutentrySuffix = ".indices"; char * gOutnamesSuffix = ".names"; void SlbListFSE(ENTRYo *entry, char *setName, int entryN, int entryCurrN) { /* dgg addition - list sequence position in file */ if ( EntryOpenData (entry)) { short entrynuminfile, seqformat, fileid; long docstart, datastart, dataend; char * filename; IDoENTRY nextid; ENTRYo *nextentry; filename= entry->file[1]->nam; fileid= 0; /* this must be set to filename entry in file of filenames ! */ entrynuminfile= entry->id->fip; /* need to look at next entry for end index !*/ docstart= entry->fip[0]; datastart= entry->fip[1]; /* !! NOTE: for GENBANK (? and others) the entry->fip currently points at the "ORIGIN" line above data. In SwissProt,EMBL it points to "SQ SEQUENCE 544 AA..." above data In PIR, it points to 'SEQUENCE' line above data. Must bypass this line here or in index users progs... */ datastart= ftell(entry->file[1]->fil); /* this is after 1st line read of EntryOpenData() */ dataend= 0; /* flag we don't know end */ /* we want real file format, in fasta/pearson lib file values */ seqformat= entry->lib->form->fil_t[1]->type - SLBxPEARSON; if (!entryCurrN || !file) { /* force output to files -- file of entry indices & file of filenames */ char *tmp, *outentry; char outDirName[FILxXNAM+1], outFile[FILxXNAM+1]; lastdocstart= 0; lastfileid= 0; nFofn = 0; maxFofn= 20; if (hashFofn) free(hashFofn); hashFofn = (long*) malloc( maxFofn * sizeof(long)); if ((tmp = ParGetStr ("tempDirName"))) sprintf (outDirName, "%s", tmp); else *outDirName = '\0'; outentry= ParGetStr("listFSE"); sprintf (outFile, "%s%s%s", outDirName, outentry, gOutentrySuffix); #if 1 _FilLN(outFile); file = fopen( outFile, "r+"); if (!file) file = fopen( outFile, "w"); else fseek(file, 0, 2); #else file = FilOpenU(outFile, &errCode); _ErrMsg2 (errCode, outFile); #endif sprintf (outFile, "%s%s%s", outDirName, outentry, gOutnamesSuffix); _FilLN(outFile); fofn = fopen( outFile, "r+"); if (!fofn) fofn = fopen( outFile, "w"); else { /* read & store hashFofn values */ char *ep, aline[FILxXNAM+20]; *aline= '\0'; while ( fgets( aline, sizeof(aline), fofn) ) { ep= aline; while (*ep && *ep != '\t' && *ep != ' ' && *ep != '\n') ep++; if (*ep) *ep= '\0'; if (nFofn >= maxFofn) { maxFofn = nFofn + 20; hashFofn= ( long*) realloc(hashFofn, maxFofn * sizeof( long)); } if (hashFofn) hashFofn[nFofn]= HashString( aline); nFofn++; } } } if (fofn) { /* !! save time by storing filenames in local array !? */ short linenum, more; long namelen; long filehash; more= 1; filehash= HashString( filename); if (hashFofn) for (linenum=0; linenumlib,"full"); /*libname= entry->lib->lnam[0]; /* short name !? */ fileid= nFofn; fseek( fofn, 0, 2); fprintf( fofn,"%s\t%d\t%d\t%s\n", filename, seqformat, fileid,libname); if (nFofn >= maxFofn) { maxFofn = nFofn + 20; hashFofn= ( long*) realloc(hashFofn, maxFofn * sizeof( long)); } if (hashFofn) hashFofn[nFofn]= filehash; nFofn++; linenum++; } } if (fileid == lastfileid && docstart == lastdocstart) goto skipListFSE; /* find data end -- shouldn't this be in entry record somewhere ! */ IdCopy( &nextid, entry->id); nextid.fip++; /* skip to next entry in library */ nextentry = EntryOpen (&nextid); if (nextentry) { if ( EntryOpenText ( nextentry) ) dataend= nextentry->fip[0]; EntryClose (&nextentry); } /* now write it all out -- use binary output to file for compactness? */ fprintf( file, "%d\t%ld\t%ld\t%ld\n", fileid, docstart, datastart, dataend); skipListFSE: /* save to screen out dups */ /* strncpy(lastename, EntryGetFullName(entry), sizeof(lastename)); */ lastfileid= fileid; lastdocstart= docstart; } if ( entryCurrN == entryN - 1 ) { if (file) { fclose (file); file = NULL; } if (fofn) { fclose(fofn); fofn= NULL; } /* dgg */ if (hashFofn) { free(hashFofn); hashFofn= NULL; } } } /*--------end ListFSE----------- */ Odd file additions ---- diff -bwrc /net/fly/b4/srs/odd/arglist.sdl odd/arglist.sdl *** /net/fly/b4/srs/odd/arglist.sdl Tue Sep 5 11:23:44 1995 --- odd/arglist.sdl Sat Sep 9 10:52:21 1995 *************** *** 68,74 **** #arg /name="-t" /parameter="printText" #arg /name="-d" /parameter="printData" #arg /name="-fse" /parameter="listFSE" ! dgg added ! #arg /name="-tdir" /parameter="tempDirName" ! dgg #arg /name="-f" /parameter="fieldList" #arg /name="-l" /parameter="libList" #arg /name="-w" /parameter="makeWild" --- 68,74 ---- #arg /name="-t" /parameter="printText" #arg /name="-d" /parameter="printData" #arg /name="-fse" /parameter="listFSE" ! dgg added ! #arg /name="-tdir" /parameter="tempDirName" ! dgg added #arg /name="-f" /parameter="fieldList" #arg /name="-l" /parameter="libList" #arg /name="-w" /parameter="makeWild" -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Thu Feb 20 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!rill.news.pipex.net!pipex!oleane!jussieu.fr!rain.fr!news.remcomp.fr!invivo!eWattel.lille From: eWattel.lille@invivo.remcomp.fr (Eric Wattel) Reply-To: eWattel.lille@invivo.remcomp.fr Newsgroups: bionet.software.srs Distribution: world Subject: DNA bending and DNA-protein interaction Date: 21 Feb 1997 10:37:13 GMT Message-ID: <154791837.2000071@invivo.remcomp.fr> Organization: inVivo Lines: 8 We would like to test bending proprieties and possible protein - DNA interaction of short DNA sequences (~35 pieces of 50-2500 pb) using an appropriate software. Mac or PC software would be welcome. Thanks in advance end ******************************************************************** Sent by inVivo. The BBS of Life Sciences, Paris, France, info@invivo.edu http://www.invivo.net/ From owner-srs@net.bio.net Thu Feb 20 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!xfer.kren.nm.kr!www.nntp.primenet.com!nntp.primenet.com!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!news From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Re: fasta and blast searches Date: 21 Feb 1997 00:03:17 GMT Organization: Biology, Indiana University - Bloomington Lines: 8 Message-ID: <5eioo5$cid@dismay.ucs.indiana.edu> References: <1997Feb20.130148@wehi> <330C7740.29EF@ebi.ac.uk> <5eio71$cff@dismay.ucs.indiana.edu> NNTP-Posting-Host: chipmunk.bio.indiana.edu I should have put this reference http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/search/subsets/SRS-Fasta-notes.html in my last post on SRS-Fasta. It describes the changes made to SRS in more detail. - don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Thu Feb 20 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!rill.news.pipex.net!pipex!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: fasta and blast searches Date: Fri, 21 Feb 1997 14:34:14 +0100 Organization: MRC Human Genome Resource Centre Lines: 21 Message-ID: <330DA456.F45@ebi.ac.uk> References: <1997Feb20.130148@wehi> <330C7740.29EF@ebi.ac.uk> <5eio71$cff@dismay.ucs.indiana.edu> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Sender: Thure Etzold X-Mailer: Mozilla 4.0b1 (Win95; I) To: Don Gilbert X-Priority: Normal Don Gilbert wrote: > > I customized version 4 of SRS to produce a file of indices > into databanks as a search result, and feed that into > FastA (which was also customized) to allow one to do > fasta searches w/o having to generate a temp data file > that was huge. Is that of any interest to you or others (the srs > customization)? I don't think I would want to run an SRS-fasta > search that allowed users to generate temp files in the multi-gigabyte > range, and even if I had that disk space, it would likely be slower > than generating byte indices. yes that is definetely of interest! I talked with Bill Pearson about your file of indices and he said he would be willing to incorporate support for it into future releases of FASTA. Did you ever contact him on this? It would much better if we could take FASTA out of the box without having to modify code. regards Thure