From owner-software@net.bio.net Mon Mar 01 22:00:00 1999 Path: biosci!CS.Arizona.EDU!newsfeed.berkeley.edu!news.maxwell.syr.edu!news.new-york.net!uunet!ffx.uu.net!in3.uu.net!nntp.snet.net!usenet From: "GREAT Success" Newsgroups: alt.comp.software.financial,bionet.software,bionet.software.pc,bit.software,biz.comp.software,comp.software,comp.sys.ibm.pc.software,comp.sys.next.software,cs.software,news.software,sb.software Subject: 15 % Restock Charge? Date: Mon, 1 Mar 1999 21:11:54 -0800 Organization: "SNET dial access service" Lines: 26 Message-ID: <7bfh7o$2ht@news1.snet.net> NNTP-Posting-Host: brpt-sh1-port74.snet.net X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 CompUSA has new signs posted in their stores. 15 % restocking charge on all opened software! The sign is much smaller than the old posted return policy! The letters are so small that you need to be right on top of the sign to see the new charges! Do you think they are trying to slip one by on us? A restock charge is fair! To sneak it in in very small print, well, that's pretty shady! I for one will never do business with them again! We only purchase around $10K/year from them, nation wide. I'm sure that's a drop in the bucket! I personally like "PC Connections", fast, less expensive, and next day delivery! I'm very satisfied with them! CompUSA, you can kiss my ass! And hey, I won't even charge you 15%! Circuit City pulled the same shit! But, not anymore! Mail order is the way to go! Send them a message!! From owner-software@net.bio.net Mon Mar 01 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!btnet-peer!btnet!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Patricia Rodriguez-Tome Newsgroups: bionet.software Subject: Biocatalog release 6.0 Date: 02 Mar 1999 18:22:17 +0000 Organization: EBI - European Bioinformatics Institute Lines: 42 Message-ID: NNTP-Posting-Host: sol6.ebi.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 920398940 2944 193.62.196.160 (2 Mar 1999 18:22:20 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 2 Mar 1999 18:22:20 GMT X-Newsreader: Gnus v5.2.25/XEmacs 20.0 Release 6.07 of the BioCatalog is now available at http://www.ebi.ac.uk/biocat/biocat.html ++++++++++Over 580 bioinformatics packages listed The BioCatalog is a software directory of general interest in molecular biology and genetics. It is not copmmercial, does not distribute software but list information on what the software is and how to retrieve it from its original place. The Text files are available from EBI anonymous FTP server at ftp://ftp.ebi.ac.uk/pub/databases/biocat This database cannot be maintained up-to-date without the help of the biocomputing community, that is to say the programs authors, archive adminsitrators and end-users. You can submit new entries describing software not already listed in the BioCatalog by filling the form at : http://www.ebi.ac.uk/biocat/biocat_form.html Thank you very much for all the submissions and corrections. enjoy Patricia -- ======================================================================= Dr. Patricia Rodriguez-Tome | URL: http://www.ebi.ac.uk R & D Coordinator The EMBL Outstation, Hinxton - The European Bioinformatics Institute Wellcome Trust genome Campus, Hinxton | Tel: +44 (0)1223 494 409 Cambridge CB10 1SD, UK | Fax: +44 (0)1223 494 468 ======================================================================== From owner-software@net.bio.net Mon Mar 01 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!unlisys!news.snafu.de!newsfeed.nacamar.de!univ-lyon1.fr!not-for-mail From: neuroviro Newsgroups: bionet.software Subject: systran software Date: Tue, 02 Mar 1999 09:50:46 +0200 Organization: C.I.S.M. Universite Claude Bernard Lyon 1 / INSA de Lyon Lines: 6 Message-ID: <36DB9855.E5DB0BF2@hotmail.com> NNTP-Posting-Host: cimacpc16.univ-lyon1.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [fr] (Macintosh; I; PPC) is there any demo version of the translator called Systran available somewhere on the net ? Thank you for your help From owner-software@net.bio.net Mon Mar 01 22:00:00 1999 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!198.138.0.5!newshub.northeast.verio.net!fu-berlin.de!vispars1.zib.DE!not-for-mail From: Hans-Christian Hege Newsgroups: bionet.biophysics,bionet.software Subject: Graduate Fellowship at ZIB, Berlin (Germany) Date: Tue, 02 Mar 1999 12:37:10 +0100 Organization: Konrad-Zuse-Zentrum (ZIB) Lines: 53 Message-ID: <36DBCD66.9056A0A4@zib.de> NNTP-Posting-Host: vispars1.zib.de (130.73.68.1) Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Access: 16 1224 1227 X-Trace: fu-berlin.de 920374630 4162 (none) 130.73.68.1 X-Mailer: Mozilla 4.5 [en] (X11; I; SunOS 5.5.1 sun4u) X-Accept-Language: en, de, de-DE, de-CH, de-AT Xref: biosci bionet.biophysics:4836 bionet.software:22969 Image Processing / Computational Geometry Graduate Fellowship Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB) Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB) invites students who are interested in pursuing a Ph.D. to apply for a fellowship in the Graduate Fellowship Program "Temperature Dependent Effects for Therapy and Diagnostics". This program is in close connection to the collaborate research centre 273 "Hyperthermia in Oncology: Methods and Clinic" at Humboldt University Berlin (speaker: Prof. Dr. R. Felix). The fellowship is available for two years with possibility of extension. The taxfree scholarship is DM 2.690,- per month for qualified students according to the regulations of the German Research Foundation (DFG). Research Areas: - algorithms for deforming anatomical grid models - algorithms for mapping grid models to medical image data - image analysis, registration and fusion Requirements: - above average masters degree (or diploma) in computer science, mathematics or physics - profound knowledge in image processing and/or computational geometry - good acquaintance with object oriented programming in C++ - interest in medical problems. We expect a high degree of commitment. In return we offer an interesting field of work, an opportunity for creativity, a highly motivated research team, excellent machinery equipment and favourable working conditions. We particularly encourage female applicants, since women are underrepresented in science and ZIB is engaged in enlarging the quota. Handicapped applicants will be preferred on terms of equal qualification. Applications with photo, curriculum vitae in tabular form and customary documents quoting the title "Graduiertenkolleg -- Scientific Visualization" should be submitted to Prof. Dr. Peter Deuflhard Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB) Takustr. 7 14195 Berlin-Dahlem Germany For further information contact Dr. Martin Seebass (seebass@zib.de, phone: +49-30-84185-328) and see http://www.zib.de/Visual. From owner-software@net.bio.net Mon Mar 01 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: "jayakumar" Newsgroups: bionet.software Subject: HI.. help on sequence analysis Date: 2 Mar 1999 13:44:10 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 23 Message-ID: <7bgpva$76a$1@mserv2.dl.ac.uk> Reply-To: "jayakumar" NNTP-Posting-Host: mserv2.dl.ac.uk Mime-Version: 1.0 Original-To: "microbiology newsgroup" , "biosoftware on bionet" content-length: 847 Return-Path: X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 X-Priority: 3 Dear Friends Does anyone know of any softwares which can check a sequence for the presence of terminators, promoters, SD sequences etc. Any suggestion will be welcome thanks in advance yours jakku **************************************************************************** ******************** R. Jayakumar, CSIR-SRF, School of Biotechnology, Madurai Kamaraj University, Madurai - 625021. India tel: +91-452-858464(hostel), 858471(ask for 374 to lab) fax: +91-452-859105 email: jakku@mrna.tn.nic.in \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\/////////// /////////////////////////////////////////////////////////////// VISIT MY WEBSITE AT http://members.tripod.com/~jakspage /////////////////////////////////////////////////////////////////\\\\\\\\\\\ \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newspump.monmouth.com!newspeer.monmouth.com!newsfeed.tli.de!newsfeed.nacamar.de!nntp.news.xara.net!xara.net!server6.netnews.ja.net!daresbury!not-for-mail From: SPhil79466@aol.com Newsgroups: bionet.software Subject: Explosive New Marketing Strategy 800 607-6006 Ex 2492 Date: 3 Mar 1999 01:06:51 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 34 Message-ID: <7bi1vb$sfd$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk content-length: 716 Return-Path: Apparently-To: This is a 1 time mailing Fire the Boss and break the Alarm Clock! I did! after eleven years, I left a $140,000 a year income for this opportunity I can truly say it was one of the best decisions of my life!!! Never commute again! make $2000-$5000 per week from home with a turn key marketing system! To find out how our system works call the 800#. You can start out in your spare time, work part time or work up to full time if you want to! It's your business! Call 1-800 607-6006 ex 2492# then press 1 no selling! stay home with the family! Proven track record of success! 1 800-607-6006 ex 2492# call now! Profit From The Internet Growth-Explosion 800 607-6006 Ex 2492 Thank You From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 From: Cornelius Krasel Subject: Re: MolBio OS? Newsgroups: bionet.software References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> User-Agent: tin/pre-1.4-980514 (UNIX) (Linux/2.0.36 (i486)) Date: Wed, 3 Mar 1999 10:09:27 +0100 Message-ID: <78uib7.55l.ln@wpxx02.toxi.uni-wuerzburg.de> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de Lines: 39 Path: biosci!agate!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.belnet.be!uni-erlangen.de!uni-wuerzburg.de!not-for-mail Andreas Milton wrote: > Actually I have experience with many OSes, but I am trying to make a decision > that impacts a large group of people. I want to accommodate all the > essential applications used in Molecular Biology. The problem I'm having is > that this field tends to be Mac and unix based. However, my gut feeling is > to go with Microsoft products because of the global acceptance of the windows > environment. Microsoft does not offer products for the Molbio market. IMO, the choice is fairly simple: If your user group is mostly GUI-based, buy Macs. If your user group consists mostly of "power users", buy Unix. Other points you might want to consider if you will have to do the administration of the machines: Macs are incredibly easy to network. Just plug them into the wall, give them an IP number and you are ready to go. On the other hand, Macs are a pain to administer because they are not intended to be multi-user machines. That is, every user can mess around with the system files, file sharing is fairly slow, etc. On the other hand, this is one of the advantages of Unix machines: you can share the file systems via NFS and you can do the administration of a whole farm of workstations from a single machine. Plus, the machines are running much more stable than any Mac or Windows machine I've seen so far. If I had to equip a lab with computers today, I would probably try to buy a host of cheap PCs running Linux and some standard software for word processing and the like (e.g. Applix). To that I'd add one "real workstation" running GCG for the more complicated molbio problems. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP4 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 From: helgi@NOSPAMdecode.is (Helgi Briem) Newsgroups: bionet.software Subject: Re: MolBio OS? Date: Wed, 03 Mar 1999 11:59:27 GMT Reply-To: helgi@NOSPAMdecode.is Message-ID: <36dd216b.1021900445@news.itn.is> References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> <78uib7.55l.ln@wpxx02.toxi.uni-wuerzburg.de> X-Newsreader: Forte Free Agent 1.11/32.235 NNTP-Posting-Host: 193.4.196.220 X-Trace: 3 Mar 1999 12:00:41 -0800, 193.4.196.220 Lines: 64 Path: biosci!agate!newsfeed.berkeley.edu!sunqbc.risq.qc.ca!wesley.videotron.net!Pollux.Teleglobe.net!news.isholf.is!193.4.196.220 On Wed, 3 Mar 1999 10:09:27 +0100, Cornelius Krasel wrote: >Andreas Milton wrote: >> Actually I have experience with many OSes, but I am trying to make a decision >> that impacts a large group of people. I want to accommodate all the >> essential applications used in Molecular Biology. The problem I'm having is >> that this field tends to be Mac and unix based. However, my gut feeling is >> to go with Microsoft products because of the global acceptance of the windows >> environment. > >Microsoft does not offer products for the Molbio market. > True, but lots of companies are now producing molbio applications for Windows and many are phasing out their Mac products. In general the NT versions are faster and far more stable than the Mac versions.. We wouldn't touch Win95/98 workstations for obvious reasons, so I cannot comment on their performance. >IMO, the choice is fairly simple: > >If your user group is mostly GUI-based, buy Macs. If your user group >consists mostly of "power users", buy Unix. > You would regret moving to Macs within a few years. >Other points you might want to consider if you will have to do the >administration of the machines: > >Macs are incredibly easy to network. Just plug them into the wall, give >them an IP number and you are ready to go. On the other hand, Macs are >a pain to administer because they are not intended to be multi-user >machines. That is, every user can mess around with the system files, >file sharing is fairly slow, etc. On the other hand, this is one of >the advantages of Unix machines: you can share the file systems via >NFS and you can do the administration of a whole farm of workstations >from a single machine. Plus, the machines are running much more stable >than any Mac or Windows machine I've seen so far. > Unix servers tend to mess up their storage of Mac files and often ruin them for use by Macs afterwards. NT on the other hand was designed from the ground up as a file server for the Mac and does a much better job of it. Far, far easier to configure too. Correctly configured NT servers are just as stable as any Unix server, but beware of NT administered by Unix specialists. >If I had to equip a lab with computers today, I would probably try to >buy a host of cheap PCs running Linux and some standard software for >word processing and the like (e.g. Applix). To that I'd add one "real >workstation" running GCG for the more complicated molbio problems. > I would use NT workstations on the desktop with a few Linux servers to run Unix applications remotely and perhaps a Sun for the things that haven't got a Linux version yet. For file serving an NT Server with a big RAID system. For running stuff like ABI sequencers you will need Macs, but the ABIs come with Macs anyway. Helgi Briem | Bioinformatics dept.| deCODE Genetics Inc. Lynghals 1 | helgi@decode.is | Tel:354-5701805 Reykjavik | IS -110 Iceland | GSM:354-8988261 From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!newsfeed.nacamar.de!dispose.news.demon.net!demon!news.demon.co.uk!demon!cammol1.demon.co.uk!r_grant From: r_grant@see.sig.for.address (Richard P. Grant) Newsgroups: bionet.software Subject: Re: MolBio OS? Date: Wed, 03 Mar 1999 08:38:02 +0000 Organization: post does not necessarily reflect the views of Cambridge Molecular Message-ID: References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> Reply-To: rgrant@netscape.net NNTP-Posting-Host: cammol1.demon.co.uk X-NNTP-Posting-Host: cammol1.demon.co.uk:212.228.79.177 X-Trace: news.demon.co.uk 920450323 nnrp-02:11221 NO-IDENT cammol1.demon.co.uk:212.228.79.177 X-Complaints-To: abuse@demon.net X-Newsreader: MT-NewsWatcher 2.4.4 X-No-ahbou: YES X-No-Archive: YES X-Face: E%wu[EoEhNnjFG!0[ 7cH@VuxC//iy$!n-+bh9Q`+SHW@&}E.&Ly(y'Tvrd5amG/o35>c3zF6QvXX, milton@san.rr.com wrote: >Actually I have experience with many OSes, but I am trying to make a decision >that impacts a large group of people. I want to accommodate all the >essential applications used in Molecular Biology. The problem I'm having is >that this field tends to be Mac and unix based. However, my gut feeling is >to go with Microsoft products because of the global acceptance of the windows >environment. that's NOT a good reason to go with MS products - they may be globally accepted (which I'd actually dispute) but that does not mean they're any good. . . Ideally you want something stonking running the GCG suite of programs under UNIX, and then hang Macs off it running some kind of X-Windows emulator . . . if money is no object. >I understand that file formats are text based... and while that does make the >migration of data quite seamless, I am still having a problem researching >what platforms people prefer in the lab... I prefer Linux and Netscape.... >but I want to make an unbiased decision. > In my experience (I've been round a few labs . . .) most molecular biologists prefer to use Macs for their daily grind, and if you have a Unix-based box running the central suite of programs (access can be via X-windows as above, or Telnet or Versaterm or Netscape) then you'll make a lot of people happy. I think the important thing is not to have to shift people away from their favoured way of doing things - if they already do things in a certain way that is. If the centralized server is not an option then go for the pile of freebies at http://iubio.bio.indiana.edu/soft/molbio/Listings.html or one of the commercial packages with a site licence. Why don't you go along to http://www.molbiol.ox.ac.uk/ for a solution that was initially set up 89/90-ish and that doesn't care what platform uses it? Factor in support costs and you'll find that a Mac-based solution will work out cheaper than Windows in the long run. And bear in mind that someone will disagree with whatever you decide . . . Richard -- Richard P. Grant MA DPhil | rgrant at cmtech.co.uk work: www.cmtech.co.uk | home: www.avnet.co.uk/adastra -- 'Bring me the hedge of Alfredo Garcia' -- From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server6.netnews.ja.net!singer.cent.gla.ac.uk!secretary1.ibls.gla.ac.uk!user From: rh@mblab.gla.ac.uk (Robert Hartley) Newsgroups: bionet.software Subject: Re: MolBio OS? Date: Wed, 03 Mar 1999 10:21:17 +0000 Organization: University of Glasgow Lines: 56 Message-ID: References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> NNTP-Posting-Host: secretary1.ibls.gla.ac.uk In article <36DCBD46.F20C8628@san.rr.com>, milton@san.rr.com wrote: > Actually I have experience with many OSes, but I am trying to make a decision > that impacts a large group of people. I want to accommodate all the > essential applications used in Molecular Biology. The problem I'm having is > that this field tends to be Mac and unix based. However, my gut feeling is > to go with Microsoft products because of the global acceptance of the windows > environment. Ok Jeff. :-) I can offer you a VERY impartial appraisal. Reason is, I prefer the amazing Acorn RiscOS running on my RiscPC600 at home but use MacG3(mainly) and sometimes wintel in work. I would consider the MacOS as the most usefull in MolBiol. (The wintel platform in my opinion has a dreadfull OS/abort retry fail). Besides, I beleive a G3 can emmulate windows to Pentium90 speed. Also Microsoft, well they have a good maketing dept. :-) If you are going for a windows enviroment consider the SGI NT workstation. I has implemented NT into the world of RISC computing and runs NT at 4x the speed of a high end CISC Pentium. To be honest I would not consider a non-RISC machine if you require speed (BUT SEE * BELOW). AND Intel have now got the ARM "StrongARM" 233Mhz chip(now at 388MHZ) RISC from an Acorn RiscPC. (This will run from two AAA bateries and can be used in a PDA) I can see the demise of the Windows dominance in general. The other alternative is to get a wintel box and put Linux on it. This could co-host with Windows and you can run a Mac Emmulator see www.ardi.com. *However the first consideration is WHAT DO YOU WANT IT TO DO? then WHAT SOFTWARE DOES THIS then WHAT DO I NEED TO RUN THIS SOFTWARE. Remember the computer is a tool to HELP you work. NOT to dictate your work. :-) These views are my OWN and not gla.ac.uk as I said I prefer something completely different. :-) Cheers Bob -- Robert Hartley BSc(Hons) Centre for Cell Engineering, IBLS Division of Infection & Immunity, Joseph Black Building, University of Glasgow, Glasgow. G12 8QQ Web: http://www.gla.ac.uk/Inter/CellEngineering E-Mail rh@mblab.gla.ac.uk Tel: +44 (0)141 3398855 Ext 2074 Fax: +44 (0) 141 330 3730 From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newshub.northeast.verio.net!newspeer.monmouth.com!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: bigben@rivendel.com Newsgroups: bionet.software Subject: Re: systran software Date: Wed, 03 Mar 1999 02:26:11 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 25 Message-ID: <7bi6jp$92$1@nnrp1.dejanews.com> References: <36DB9855.E5DB0BF2@hotmail.com> NNTP-Posting-Host: 209.24.165.32 X-Article-Creation-Date: Wed Mar 03 02:26:11 1999 GMT X-Http-User-Agent: Mozilla/4.06 [en] (Win95; I) X-Http-Proxy: 1.0 x5.dejanews.com:80 (Squid/1.1.22) for client 209.24.165.32 In article <36DB9855.E5DB0BF2@hotmail.com>, neuroviro wrote: > is there any demo version of the translator called Systran available > somewhere on the net ? > The translation system on AltaVista search engine is Systran. That system is called Babelfish and you can give it a test online at: http://babelfish.altavista.digital.com/cgi-bin/translate?urltext= Best Regards, Bennett (Bigben) Site Coordinator Rivendell Language Resources Online Dictionaries and Translators http://rivendel.com/~ric/resources/dictionary.html Machine Translation Systems http://rivendel.com/~ric/resources/mt.html -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!CMMT.UBC.CA!francis From: francis@CMMT.UBC.CA Newsgroups: bionet.software Subject: Re: exon/intron prediction Date: 3 Mar 1999 08:22:07 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <199903031612.IAA10854@monod.cmmt.ubc.ca> NNTP-Posting-Host: net.bio.net > From: Clemens Suter-Crazzolara > Subject: exon/intron prediction > I am preparing a course, and therfore I am looking for programmes that > allow intron/exon prediction. Until now I have found: genscan, frames, > xpound, codonpreference, testcode, fgenes, orffinder and genlang. > > Are there other programmes for this purpose out there ? > > Thanks in advance, if possible mail to my e-mail address. Jack Jenuth from base4 put together such a list, and put it up on their www page, you may want to look at that. http://telomere.base4.com/html/Joes_orfs.html cheers, f. -- | B.F. Francis Ouellette tel: (604) 875-3815 | | Director, Bioinformatics Core Facility fax: (604) 875-3800 | | Centre for Molecular Medicine and Therapeutics, UBC, Canada | | francis@cmmt.ubc.ca | From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!news.stanford.edu!news.ems.psu.edu!news.cis.ohio-state.edu!malgudi.oar.net!storm.twcol.com!chnws02.mediaone.net!192.148.253.68!netnews.com!news.idt.net!fu-berlin.de!News.CoLi.Uni-SB.DE!news-kar1.dfn.de!news.embl-heidelberg.de!news.dkfz-heidelberg.de!not-for-mail From: Clemens Suter-Crazzolara Newsgroups: bionet.software,bionet.molbio.methds-reagnts Subject: exon/intron prediction Date: Wed, 03 Mar 1999 15:55:36 +0100 Organization: DKFZ Heidelberg Lines: 13 Message-ID: <36DD4D68.48CD29C2@dkfz-heidelberg.de> NNTP-Posting-Host: mbp-sun13.inet.dkfz-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.inet.dkfz-heidelberg.de 920472962 680 193.174.59.135 (3 Mar 1999 14:56:02 GMT) X-Complaints-To: usenet@news.dkfz-heidelberg.de NNTP-Posting-Date: 3 Mar 1999 14:56:02 GMT X-Mailer: Mozilla 4.04 [en] (X11; I; SunOS 5.5 sun4m) Xref: biosci bionet.software:22982 bionet.molbio.methds-reagnts:74439 Hello, I am preparing a course, and therfore I am looking for programmes that allow intron/exon prediction. Until now I have found: genscan, frames, xpound, codonpreference, testcode, fgenes, orffinder and genlang. Are there other programmes for this purpose out there ? Thanks in advance, if possible mail to my e-mail address. Clemens Suter-Crazzolara Bioinformatics, DKFZ Heidelberg From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newspeer.monmouth.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!mole.bio.cam.ac.uk!jacp1 From: jacp1@mole.bio.cam.ac.uk (Justin Powell) Newsgroups: bionet.software Subject: Re: MolBio OS? Date: 3 Mar 1999 14:23:16 GMT Organization: University of Cambridge, England Lines: 9 Message-ID: <7bjgkk$jgh$1@pegasus.csx.cam.ac.uk> References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> <78uib7.55l.ln@wpxx02.toxi.uni-wuerzburg.de> <36dd216b.1021900445@news.itn.is> <1kdjb7.p9n.ln@wpxx02.toxi.uni-wuerzburg.de> NNTP-Posting-Host: mole.bio.cam.ac.uk X-Newsreader: NN version 6.5.0 #3 (NOV) Our lab is planning to obtain a new computer for doing bioinformatics work, currently we use our own macs and unix boxes belonging to the department. We do mainly homology searches, protein motif searches, function prediction and possibly some structural prediction. It seems to me that the main determinant in our decision is is there any software which we are likely to want to use in future which needs a unix box to run on, or is everything available over the web these days? Justin Powell From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.cwix.com!204.210.0.20!news.san.rr.com!not-for-mail Message-ID: <36DCBD46.F20C8628@san.rr.com> From: Andreas Milton Reply-To: milton@san.rr.com Organization: yeah right! X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software Subject: Re: MolBio OS? References: <36DB7DBD.51B54998@san.rr.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 69 Date: Tue, 02 Mar 1999 20:40:38 -0800 NNTP-Posting-Host: 204.210.36.165 X-Trace: news.san.rr.com 920436367 204.210.36.165 (Tue, 02 Mar 1999 20:46:07 PDT) NNTP-Posting-Date: Tue, 02 Mar 1999 20:46:07 PDT Actually I have experience with many OSes, but I am trying to make a decision that impacts a large group of people. I want to accommodate all the essential applications used in Molecular Biology. The problem I'm having is that this field tends to be Mac and unix based. However, my gut feeling is to go with Microsoft products because of the global acceptance of the windows environment. I understand that file formats are text based... and while that does make the migration of data quite seamless, I am still having a problem researching what platforms people prefer in the lab... I prefer Linux and Netscape.... but I want to make an unbiased decision. ---thanks for your assistance. Jeff "Richard P. Grant" wrote: > In article <36DB7DBD.51B54998@san.rr.com>, milton@san.rr.com wrote: > > >I'm really interested in finding some information on what platforms > >people use in Molecular Biology... as I am currently having to grapple > >with this decision. > > > >What operating system do you use? > > > > Mac > > >What operating system would you prefer? > > > Mac > > >What browser do you prefer? > > > > > NS4.5 > > >It's unfortunate when a platform communication barrier gets in the way > >of real research. > > Seeing as most molbiol programs exchange data in a text formatof one sort > or another this is not really a problem. > > >"...time to decide." > > > >Any suggestions are greatly appreciated. > > I would suggest that you pick the platform with which you are most > familiar/happy/most productive on. If you find you're not fighting the > machine then your work will go more smoothly, and there is in fact a pile > of molbiol software for all the platforms (except possibly Amstrad (-: ). > > Is your problem that you have no experience of different OSes or that > you're not being allowed to have your first choice? Or something else? > > Followups set. > > Cheers, > > Richard > > -- > Richard P. Grant MA DPhil | rgrant at cmtech.co.uk > work: www.cmtech.co.uk | home: www.avnet.co.uk/adastra > -- Doctorum Adamus cum Flabello Dulci -- From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!diablo.theplanet.net!dispose.news.demon.net!demon!news.demon.co.uk!demon!cammol1.demon.co.uk!r_grant From: r_grant@see.sig.for.address (Richard P. Grant) Newsgroups: bionet.software Subject: Re: MolBio OS? Date: Wed, 03 Mar 1999 12:28:43 +0000 Organization: post does not necessarily reflect the views of Cambridge Molecular Message-ID: References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> <78uib7.55l.ln@wpxx02.toxi.uni-wuerzburg.de> <36dd216b.1021900445@news.itn.is> Reply-To: rgrant@netscape.net NNTP-Posting-Host: cammol1.demon.co.uk X-NNTP-Posting-Host: cammol1.demon.co.uk:212.228.79.177 X-Trace: news.demon.co.uk 920464156 nnrp-02:18081 NO-IDENT cammol1.demon.co.uk:212.228.79.177 X-Complaints-To: abuse@demon.net X-Newsreader: MT-NewsWatcher 2.4.4 X-No-ahbou: YES X-No-Archive: YES X-Face: E%wu[EoEhNnjFG!0[ 7cH@VuxC//iy$!n-+bh9Q`+SHW@&}E.&Ly(y'Tvrd5amG/o35>c3zF6QvXX, helgi@NOSPAMdecode.is wrote: >True, but lots of companies are now producing molbio >applications for Windows and many are phasing out their >Mac products. On what do you base that statement? (I'm not making any comment about NT vs Mac software performance because I've never tried running molbiol software on NT. My only experience with NT is extremely bad) >You would regret moving to Macs within a few years. On what basis do you make that inflammatory statement? >Unix servers tend to mess up their storage of Mac files and >often ruin them for use by Macs afterwards. NT on the other >hand was designed from the ground up as a file server for >the Mac and does a much better job of it. Sorry, this is utter crap. Where are you getting your data? I'd go for Unix over NT any day of the week. > but beware of NT administered >by Unix specialists. I'd turn that statement on its head. I'd also beware of NT machines adminstered by NT specialists. >running stuff like ABI sequencers you will need Macs, but >the ABIs come with Macs anyway. Generally over-powered Macs that ABI recommend you don't use for anything else. Get some iMacs, they're real cheap now and ideal for a networked environment. R -- Richard P. Grant MA DPhil | rgrant at cmtech.co.uk work: www.cmtech.co.uk | home: www.avnet.co.uk/adastra -- In Ventum Faciens Aquam -- From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!netnews1.nw.verio.net!netnews.nwnet.net!socal.verio.net!nntp.ni.net!news.service.uci.edu!usenet From: Harry Mangalam Newsgroups: bionet.software Subject: Local BLAST server - any experience on dual/quad Intel - Linux platforms Date: Wed, 03 Mar 1999 09:55:49 -0800 Organization: UC Irvine Lines: 22 Message-ID: <36DD77A4.A62F9B42@uci.edu> NNTP-Posting-Host: cx408397-a.irvn1.occa.home.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.32 i686) X-Accept-Language: en Hi - I've been asked to eval setting up a local BLAST server. For compatibility with other requirements, the OS will be Linux, unless someone can give me extremely good reasons not to. I'm considering using a dual Pentium II/Celeron, unless I can get feedback that BLAST does not work well on such a system, in which case we would run either a uni-PII/Celeron or if more $ can be scraped up, an Alpha (but having experience with Linux/Alpha, I know some of the problems with that approach). So, does anyone out there have experience with BLAST on an SMP Intel box (dual or quad (PPro or Xeon - I know that PII's can't go there) and if so, on what kernel and what were the gotchas? Also rec's on minimum memory for maximum efficiency would be appreciated. -- Cheers, Harry Harry J Mangalam -- (949) 856 2899 -- mangalam@home.com From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news-peer1.sprintlink.net!news-in-east1.sprintlink.net!news.sprintlink.net!itssrv1.ucsf.edu!mac-daddy.ucsf.edu!user From: bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD) Newsgroups: bionet.software Subject: Re: MolBio OS? Date: Wed, 03 Mar 1999 15:16:11 -0800 Organization: University of California, San Francisco Lines: 50 Message-ID: References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> <78uib7.55l.ln@wpxx02.toxi.uni-wuerzburg.de> <36dd216b.1021900445@news.itn.is> <1kdjb7.p9n.ln@wpxx02.toxi.uni-wuerzburg.de> NNTP-Posting-Host: mac-daddy.ucsf.edu In article <1kdjb7.p9n.ln@wpxx02.toxi.uni-wuerzburg.de>, Cornelius Krasel wrote: > To put this soon-to-be OS flame war into a geographical perspective, one > should hasten to add that most European labs tend to use Win* computers > where U.S. labs tend to use Macs. The reason is simply that Apple USA > has been much more supportive to the academic environment (and to customers > in general) than for example Apple Germany. iMacs in the U.S. are priced > competitively; iMacs in Germany are not. > --Cornelius. A good reminder. In the labs I worked in or visited in the UK I found that many people used PCs but *wanted* Macs (this was in the days of Win3.1 and before widescale networking). Another phenomenon I noticed is that there appears to be an east/west split in the U.S. when it comes to academic computing with a preponderence of PCs on the east coast and Macs on the west. I am told this is because Apple's donation of Macs to schools was predominantly in the west. From observation people tend to be passionately loyal to Macs, Linux, BSD, Solaris x86, OS/2, plain DOS, BeOS etc. and there are good newsgroups for all. I have yet to hear anyone express loyalty towards Win9x or NT but hear a great deal of criticism by those who have to maintain them - "they are there - just *deal* with them". Judge all posts accordingly. I know of no "must have" molbio applications for Win9x. There are some nice programs that run with Win3.1x but these don't need Win9x. There is an enormous amount of good UNIX open source molbio software available that can be compiled with open source tools (eg. gcc or egcs) so is available for Linux, FreeBSD, Solaris and DOS (using DJGPP). There don't appear to be any good cheap PC equivalents of DNA Strider (GeneRunner was getting there before it disappeared) or MacPlasMap (although I do like Plasmid Processor). Have fun, Bernard [Home: Linux, Solaris, DOS/Win3.11 Work: Mac, Win95] -- Bernard P. Murray, PhD Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!news.maxwell.syr.edu!newsfeed.cwix.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: Lchauvet74@aol.com Newsgroups: bionet.general,bionet.jobs.wanted,bionet.molbio.proteins.fluorescent,bionet.software Subject: French Bio-Med AND Informatics/Programming : I need an you! Date: Wed, 03 Mar 1999 22:11:04 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 49 Message-ID: <7bkc1f$sp9$1@nnrp1.dejanews.com> NNTP-Posting-Host: 152.173.188.216 X-Article-Creation-Date: Wed Mar 03 22:11:04 1999 GMT X-Http-User-Agent: Mozilla/4.0 (compatible; MSIE 4.01; Windows 95) X-Http-Proxy: 1.1 x16.dejanews.com:80 (Squid/1.1.22) for client 152.173.188.216 Xref: biosci bionet.general:32562 bionet.jobs.wanted:27613 bionet.molbio.proteins.fluorescent:2549 bionet.software:22988 Hello, I am a french student, and I am currently finishing an Advanced Professional Degree in Computer Sciences (Major Microscopic Imaging). and my course ends with a training period of at least three months (contract from the start of July until the end of September... but I can stay longer) in a company. From this course, I acquired:  an ability to quickly adapt myself to different programming languages,  a precise understanding of computer systems' functions, regarding software and hardware,  a good knowledge of the problems specific to software engineering (project managing, modeling, database building and managing). Also, I chose the Microscopy Imaging optional module which allowed me to have solid abilities regarding the differents systems for image acquisition (microscopy X-ray, confocal, electronic and optic) and image processing methods. This computing skills come in addition to a solid biological background: I have a Master degree Cells Biology and Physiology, giving me the possibility to analyse objectively biological problems. Interested for a long time in image analysis, I took on a temporary research fellowship in CNRS (Undergraduate level), regarding image analyses methods for the study of red blood cells deformation. I am currently working on the complete conception of a software for analysing image sequences using an algorithm of optical flow, within the framework of my course. Eventually, my professional aim is concerned with the conception of computing systems applied to life sciences (medical applications, structural biochemistry, biology, pharmacology). Aware of your products and activity in this domain, I am able to bring to you my skills as a trainee and thereby take profit of your experience in order to achieve my professional aim. If you have any opportunity for an internship in this field, please send me an e-mail (my address is Lchauvet74@aol.com) . If you wish to get more informations about my education, take a look at my resume on my Web site at this address : http://www.multimania.com/chauvetl/ Thanks, Laurent CHAUVET -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!su-news-hub1.bbnplanet.com!news.gtei.net!news.pbi.net!207.33.1.6!news.he.net!mercury.cts.com!socal.verio.net!nntp.ni.net!news.service.uci.edu!usenet From: Harry Mangalam Newsgroups: bionet.software Subject: Re: HI.. help on sequence analysis Date: Wed, 03 Mar 1999 10:35:11 -0800 Organization: UC Irvine Lines: 39 Message-ID: <36DD80DF.107E0BB1@uci.edu> References: <7bgpva$76a$1@mserv2.dl.ac.uk> NNTP-Posting-Host: cx408397-a.irvn1.occa.home.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.32 i686) X-Accept-Language: en If you can define them in IUPAC codes, tacg can find them (with specified # of errors, in degenerate sequence of any length). If you want to run the commandline app, you can download it at: ftp://mamba.bio.uci.edu/pub/tacg If you want to use the somewhat less capable, but easier-to-use Web interface, you can go to: http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg2.form.html But you'll have to upload your own GCG-REBASE formatted file containing the sequences you want to find. There's an example of what you have to do there. Alternatively, there are many such programs that can do this, depending on your sequence length (is is a KB or multiple Megabases?), complexity of patterns (do you need to be able to search for a regular expression? and IUPAC expression? a profile? with errors? both strands simultaneously?), number of patters to search for at once time, whether you need to be able to handle degenerate sequence input, etc. - the 'grep/egrep/agrep' family of regular expression matchers may be good enough for you. - grepseq is a very fast biosequence version of agrep, but has some interface peculiarities. - GCG's findpatterns is quite robust but it's ... GCG, and $ware. - DNAStrider and most commercial apps have such capabilities built in, but (strangely) many don't allow searching with errors or even with IUPAC codes or even regular expressions. jayakumar wrote: > Does anyone know of any softwares which can check a sequence for the > presence of terminators, promoters, SD sequences etc. -- Cheers, Harry Harry J Mangalam -- (949) 856 2899 -- mangalam@home.com From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!masternews.telia.net!News.Amsterdam.UnisourceCS!news.klaus-datentechnik.de!news From: "LogicX Software Development" Newsgroups: bionet.software Subject: LogicX Software Development Date: Wed, 3 Mar 1999 19:00:44 +0100 Organization: Kunde von Klaus Datentechnik GmbH Lines: 7 Message-ID: <7bjtfb$l7l@news.kdt.de> NNTP-Posting-Host: line46.kdt.de X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Ist eine Software Entwicklungsfirma in Deutschland eMail: LogicX@wtal.de Homepage: http://home.wtal.de/UDO/LogicX From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 From: Cornelius Krasel Subject: Re: MolBio OS? Newsgroups: bionet.software References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> <78uib7.55l.ln@wpxx02.toxi.uni-wuerzburg.de> <36dd216b.1021900445@news.itn.is> User-Agent: tin/pre-1.4-980514 (UNIX) (Linux/2.0.36 (i486)) Date: Wed, 3 Mar 1999 14:31:45 +0100 Message-ID: <1kdjb7.p9n.ln@wpxx02.toxi.uni-wuerzburg.de> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de Lines: 42 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.tli.de!newsfeed.nacamar.de!uni-erlangen.de!uni-wuerzburg.de!not-for-mail Helgi Briem wrote: > On Wed, 3 Mar 1999 10:09:27 +0100, Cornelius Krasel > wrote: >>Microsoft does not offer products for the Molbio market. > > True, but lots of companies are now producing molbio > applications for Windows and many are phasing out their > Mac products. In general the NT versions are faster > and far more stable than the Mac versions.. We wouldn't > touch Win95/98 workstations for obvious reasons, so I cannot > comment on their performance. I cannot say much about Molbio applications for desktop machines since I touched the last demo versions maybe four to five years ago and I assume (and hope) that they have advanced from there. It is, however, clear that a PowerPC delivers more raw speed to a desktop computer than a similarly priced Pentium chip. Therefore, the claim that "NT versions are faster" than Mac versions is something which I find a bit difficult to swallow. It is true that NT is probably more stable since Apple has still not managed to implement a sensible memory protection system into MacOS 8.5. > Unix servers tend to mess up their storage of Mac files and > often ruin them for use by Macs afterwards. We have a Linux box set up as a Mac fileserver and there have been no problems so far. To put this soon-to-be OS flame war into a geographical perspective, one should hasten to add that most European labs tend to use Win* computers where U.S. labs tend to use Macs. The reason is simply that Apple USA has been much more supportive to the academic environment (and to customers in general) than for example Apple Germany. iMacs in the U.S. are priced competitively; iMacs in Germany are not. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP4 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!howland.erols.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Keith James Newsgroups: bionet.software Subject: Re: MolBio OS? Date: 03 Mar 1999 17:53:46 +0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 37 Message-ID: References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> <78uib7.55l.ln@wpxx02.toxi.uni-wuerzburg.de> <36dd216b.1021900445@news.itn.is> <1kdjb7.p9n.ln@wpxx02.toxi.uni-wuerzburg.de> <7bjgkk$jgh$1@pegasus.csx.cam.ac.uk> NNTP-Posting-Host: fes6.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 920483627 27654 193.60.84.41 (3 Mar 1999 17:53:47 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 3 Mar 1999 17:53:47 GMT X-Newsreader: Gnus v5.5/Emacs 20.3 >>>>> "Justin" == Justin Powell writes: Justin> Our lab is planning to obtain a new computer for doing Justin> bioinformatics work, currently we use our own macs and Justin> unix boxes belonging to the department. We do mainly Justin> homology searches, protein motif searches, function Justin> prediction and possibly some structural prediction. It Justin> seems to me that the main determinant in our decision is Justin> is there any software which we are likely to want to use Justin> in future which needs a unix box to run on, or is Justin> everything available over the web these days? I'm going to refrain from making any OS recommendations in this thread as the pros and cons have been summed up pretty well already. (*nix.. oops, I couldn't help myself). Given the same task two people may approach it with very different tools and achieve the same result. One may like to point and click, while the other will do the same analysis by shoving the data through a shell script, and never the 'twain shall meet etc. All the better if you can provide for both. It's relatively easy to recreate a foreign GUI style on Linux, but a thankless task trying to recreate Unix scripting on NT or a Mac. grepping yesterday's release of the EBI Biocatalog (combined open source, *ware & commercial) for OS support: Unix/Sun 234, Win 64, Mac 60, DOS 59, VAX 41 The disadvantage of relying heavily on web-based services are the obvious ones; services may come and go, slow responses, inefficient data input through browers. -- Keith James -- kdj@sanger.ac.uk -- http://www.sanger.ac.uk/Users/kdj The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA From owner-software@net.bio.net Wed Mar 03 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!sunqbc.risq.qc.ca!cyclone.mbnet.mb.ca!canopus.cc.umanitoba.ca!not-for-mail From: Brian Fristensky Newsgroups: bionet.software Subject: Re: MolBio OS? Date: Wed, 03 Mar 1999 20:20:35 -0600 Organization: University of Manitoba Lines: 58 Message-ID: <36DDEDF3.F9E6970@cc.umanitoba.ca> References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> NNTP-Posting-Host: brassica.cc.umanitoba.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: canopus.cc.umanitoba.ca 920514036 26871 130.179.16.121 (4 Mar 1999 02:20:36 GMT) X-Complaints-To: Postmaster@cc.umanitoba.ca NNTP-Posting-Date: 4 Mar 1999 02:20:36 GMT X-Mailer: Mozilla 4.06 [en] (X11; U; SunOS 5.5.1 sun4u) Andreas Milton wrote: > > Actually I have experience with many OSes, but I am trying to make a decision > that impacts a large group of people. I want to accommodate all the > essential applications used in Molecular Biology. The problem I'm having is > that this field tends to be Mac and unix based. However, my gut feeling is > to go with Microsoft products because of the global acceptance of the windows > environment. > > I understand that file formats are text based... and while that does make the > migration of data quite seamless, I am still having a problem researching > what platforms people prefer in the lab... I prefer Linux and Netscape.... > but I want to make an unbiased decision. > When I did set up my lab in 1990, I decided that is did NOT want to support multiple OSes, not just because of the knowledge and time required to master and work with each different OS, but also because I wanted to avoid fragmentation of data. That is, I didn't want data scattered across different machines, in different versions and formats. I wanted wanted things to be easily accessible across a network. I chose Sun Unix, and have been enjoying it ever since. Our lab runs on the thin client model, where everything resides on the server, and people login via X-terminals. There's no such thing as hard disk crashses destroying data, no competetion to get onto a particular PC that has important data or programs. Anyone can do anything from any terminal. I won't go into all the details for it, because I have an entire Web site on the subject: http://home.cc.umanitoba.ca/~psgendb P.S. One response to this post suggested that it may not be necessary to consider whether Mol. Bio. programs ran on your desktop OS, because everything was available at Web sites anyway. I couldn't disagree more. Web browsers are convenient for Web browsing, but the Web interface is extremely limited, compared to a fully integrated desktop. For anything other than the most trivial tasks with a single sequence, you need the convenience of being able to work with locally-installed software in your own directory hierarchy. =============================================================================== Brian Fristensky | What a vast abyss Department of Plant Science | can separate falutist from cadenza played, University of Manitoba | huffing maker from the vial made, Winnipeg, MB R3T 2N2 CANADA | the lover and the kiss. frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Phyllis Janowitz (1996) FAX: 204-261-5732 | His Apologia Pro Ratiocination http://home.cc.umanitoba.ca/~frist/ THE LAUREL REVIEW 30(1) =============================================================================== From owner-software@net.bio.net Wed Mar 03 22:00:00 1999 Message-ID: <36DE8519.B970285F@decode.is> Date: Thu, 04 Mar 1999 13:05:29 +0000 From: "Baldur Már Bragason" X-Mailer: Mozilla 4.05 [en] (WinNT; I) MIME-Version: 1.0 Newsgroups: bionet.software Subject: Secondary Structure Prediction Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: 193.4.196.220 X-Trace: 4 Mar 1999 13:04:37 -0800, 193.4.196.220 Lines: 9 Path: biosci!agate!newsfeed.berkeley.edu!sunqbc.risq.qc.ca!wesley.videotron.net!Pollux.Teleglobe.net!news.isholf.is!193.4.196.220 HI What are the best 2D predictors availible ? I am both looking for general predictors and specialized, such as only for helices, strands etc. Baldur Mar Bragason From owner-software@net.bio.net Wed Mar 03 22:00:00 1999 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Miriam Hirshberg Newsgroups: bionet.software Subject: Secondary Structure Prediction Date: 4 Mar 1999 13:57:14 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 28 Message-ID: <7bm3fq$7d1$1@mserv2.dl.ac.uk> Reply-To: m.hirshberg@mole.bio.cam.ac.uk NNTP-Posting-Host: mserv2.dl.ac.uk Original-To: bio-software@dl.ac.uk content-length: 715 Return-Path: > > >HI > >What are the best 2D predictors availible ? >I am both looking for general predictors and specialized, such as only >for helices, strands etc. > >Baldur Mar Bragason > > there are many try for example Jpred on http://circinus.ebi.ac.uk:8081/ Miri ====================================================================== Miriam (Miri) Hirshberg e-mail: m.hirshberg@mole.bio.cam.ac.uk Department of Biochemistry Tel : (+44) 01223 766018 University of Cambridge Tel : (+44) 01223 333600 (switch board) 80 Tennis Court Road Fax : (+44) 01223 766002 Old Addenbrooke's Site Cambridge CB2 1GA, UK ======================================================================= From owner-software@net.bio.net Wed Mar 03 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.concentric.net!news.he.net!news.pagesat.net!news.itis.com!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Re: MolBio OS? Date: 4 Mar 1999 02:49:00 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 24 Sender: reguser@ebv.oncology.wisc.edu Message-ID: References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> <78uib7.55l.ln@wpxx02.toxi.uni-wuerzburg.de> <36dd216b.1021900445@news.itn.is> <1kdjb7.p9n.ln@wpxx02.toxi.uni-wuerzburg.de> Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: ebv.oncology.wisc.edu User-Agent: slrn/0.9.5.4 (UNIX) On Wed, 03 Mar 1999 15:16:11 -0800, Bernard P. Murray, PhD (bpmurray*STUFFER*@socrates.ucsf.edu) wrote: For an "OS-war", your thoughts were stated very objectively! >There don't appear to be any good cheap PC equivalents >of DNA Strider (GeneRunner was getting there before >it disappeared) or MacPlasMap (although I do like >Plasmid Processor). For what its worth, DNA Strider (v 1.2) does run under Executor/Linux and Executor/DOS. And if you currently use a multi-boot Linux/Win32 system, take a look at VMWare, which is due to debut at LinuxWorld. They claim to run Linux and NT *concurrently*. http://www.vmware.com Later, Ashok -- Ashok Aiyar, Ph.D. McArdle Laboratory for Cancer Research aiyar@ebv.oncology.wisc.edu From owner-software@net.bio.net Wed Mar 03 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.tli.de!newsfeed.nacamar.de!dispose.news.demon.net!demon!news.demon.co.uk!demon!cammol1.demon.co.uk!r_grant From: r_grant@see.sig.for.address (Richard P. Grant) Newsgroups: bionet.software Subject: Re: MolBio OS? Date: Thu, 04 Mar 1999 15:59:55 +0000 Organization: post does not necessarily reflect the views of Cambridge Molecular Message-ID: References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> <36DE9FD2.2B9E24C@pitt.edu> Reply-To: rgrant@netscape.net NNTP-Posting-Host: cammol1.demon.co.uk X-NNTP-Posting-Host: cammol1.demon.co.uk:212.228.79.177 X-Trace: news.demon.co.uk 920563227 nnrp-09:19192 NO-IDENT cammol1.demon.co.uk:212.228.79.177 X-Complaints-To: abuse@demon.net X-Newsreader: MT-NewsWatcher 2.4.4 X-No-ahbou: YES X-No-Archive: YES X-Face: E%wu[EoEhNnjFG!0[ 7cH@VuxC//iy$!n-+bh9Q`+SHW@&}E.&Ly(y'Tvrd5amG/o35>c3zF6QvXX, rdudley+@pitt.edu wrote: > You'll get the same >crap about power drills, too. Although not many people dare to tell me my Bosch hammer drill doesn't work . . . ;-) -- Richard P. Grant MA DPhil | rgrant at cmtech.co.uk work: www.cmtech.co.uk | home: www.avnet.co.uk/adastra -- 'Bring me the hedge of Alfredo Garcia' -- From owner-software@net.bio.net Wed Mar 03 22:00:00 1999 Path: biosci!USA.NET!goldbrg6 From: goldbrg6@USA.NET ("Gary") Newsgroups: bionet.software Subject: Weight Loss Products. Date: 4 Mar 1999 14:34:07 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <199903042215.XAA02152@juniper.es> NNTP-Posting-Host: net.bio.net Bargains Dream Homes are had by buying Houses or Condos direct from an owner, including low down payments ! Get your listing now. Call 716-387-8300 for details 24 hours/7 days, for Image # 198. Free "For Sale By Owner" Advertising for owners of Houses or Condo ? Save $$$ thousands in Realtor fees. Limited time only 100% free, no charge ever offer. 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Call 716-387-8300 for details 24 hours/7 days, for Image # 194. remove at: mailto:kane90998@yahoo.com?subject=remove From owner-software@net.bio.net Wed Mar 03 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!cyclone.bc.net!newsfeed.bctel.net!news.bctel.net!not-for-mail Message-ID: <36DEFA70.FFD1395D@terryfox.ubc.ca> From: Paul Kowalski Reply-To: paul@REMOVE.terryfox.ubc.ca Organization: BC Cancer Agency X-Mailer: Mozilla 4.06 [en] (WinNT; I) MIME-Version: 1.0 Newsgroups: bionet.software.gcg,bionet.software Subject: GCG-telnet timeout thru firewall Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 14 Date: Thu, 04 Mar 1999 13:26:09 -0800 NNTP-Posting-Host: 204.174.218.234 X-Complaints-To: news@bctel.net X-Trace: news.bctel.net 920582895 204.174.218.234 (Thu, 04 Mar 1999 13:28:15 PDT) NNTP-Posting-Date: Thu, 04 Mar 1999 13:28:15 PDT Xref: biosci bionet.software.gcg:3438 bionet.software:23000 Hi - this isn't a specific GCG problem..... Is there a unix program or perhaps a Windows program which would prevent a Firewall-induced timeout on a telnet connection to GCG? Analogous to "stay-alive" applets for keeping dialin connections from autodisconnecting. Thanks in advance- -- Paul Kowalski, PhD Terry Fox Laboratory, BCCA paul@terryfox.ubc.ca pkowalsk@bccancer.bc.ca From owner-software@net.bio.net Wed Mar 03 22:00:00 1999 Path: biosci!UCONNVM.UCONN.EDU!knecht From: knecht@UCONNVM.UCONN.EDU (David Knecht) Newsgroups: bionet.software Subject: introns in DNA programs Date: 4 Mar 1999 09:40:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net We are trying to display DNA sequence, derived protein sequence and introns in a publication type figure. None of the Mac programs I have or have demo's of know how to find or display introns so that the protein translation ignores that region of the gene when displayed. Do any of the current programs #1 find introns, or #2, know how to create a display that deals with them correctly. Thanks- Dave Dr. David Knecht Department of Molecular and Cell Biology University of Connecticut 75 N. Eagleville Rd. U-125 Storrs, CT 06269 Knecht@uconnvm.uconn.edu 860-486-2200 860-486-4331 (fax) From owner-software@net.bio.net Wed Mar 03 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!logbridge.uoregon.edu!newsswitch.lcs.mit.edu!rill.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!HEAnet!web3.tcd.ie!acer.gen.tcd.ie!tpwalsh From: tpwalsh@acer.gen.tcd.ie (Urmhumhan) Newsgroups: bionet.software Subject: Re: Secondary Structure Prediction Date: 4 Mar 1999 16:36:14 GMT Organization: Urmhumhan Lines: 19 Message-ID: <7bmcpu$rhp@web3.tcd.ie> References: <7bm3fq$7d1$1@mserv2.dl.ac.uk> NNTP-Posting-Host: acer.gen.tcd.ie m.hirshberg@mole.bio.cam.ac.uk wrote: >> >>What are the best 2D predictors availible ? >>I am both looking for general predictors and specialized, such as only >>for helices, strands etc. > >there are many try for example > >Jpred on http://circinus.ebi.ac.uk:8081/ Two of the best are: PHD: http://www.embl-heidelberg.de/predictprotein/ppDoPred.html DSC: http://bonsai.lif.icnet.uk/bmm/dsc/ TW From owner-software@net.bio.net Wed Mar 03 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: TopMan6304@aol.com Newsgroups: bionet.software Subject: Serious? Date: 4 Mar 1999 03:43:27 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 115 Message-ID: <7bkvgv$hlr$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk content-length: 4895 Return-Path: Apparently-To: TO REMOVE YOUR EMAIL ADDRESS, CALL 1 (800) 242-0363 #2155. --------------------------------------------------------------- IF YOU ARE SERIOUS ABOUT PROMOTING A PRODUCT, A SERVICE, A BUSINESS, OR A SITE ON THE NET, YOU NEED TO READ THIS MAILER! ================================================================== We offer an affordable range of unique softwares, services & products to help you to achieve your above objectives! ---------------------------------------------------------- 1)SOFTWARES: ___________ A)SENSOR PLUS!: a new & unique software that identifies a visitor to your site by detecting and grabbing the e-mail address of visitors to your site, and sending the visitors an email from you thanking them for the visit, and offering specials, etc. Try SENSOR PLUS! 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From owner-software@net.bio.net Wed Mar 03 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!portc02.blue.aol.com!pitt.edu!not-for-mail From: Rich Dudley Newsgroups: bionet.software Subject: Re: MolBio OS? Date: Thu, 04 Mar 1999 09:59:31 -0500 Organization: University of Pittsburgh, Dept. of Cell Biology and Physiology Lines: 56 Message-ID: <36DE9FD2.2B9E24C@pitt.edu> References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> Reply-To: rdudley+@pitt.edu NNTP-Posting-Host: whill.cbp.pitt.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en Andreas Milton wrote: > Actually I have experience with many OSes, but I am trying to make a decision > that impacts a large group of people. I want to accommodate all the > essential applications used in Molecular Biology. The problem I'm having is > that this field tends to be Mac and unix based. However, my gut feeling is > to go with Microsoft products because of the global acceptance of the windows > environment. > > I understand that file formats are text based... and while that does make the > migration of data quite seamless, I am still having a problem researching > what platforms people prefer in the lab... I prefer Linux and Netscape.... > but I want to make an unbiased decision. > > ---thanks for your assistance. > > Jeff If you have a couple of computers you can use, I would call some software vendors and get demos of their software. Let all the PIs play around and go with what they like the best. I am partial to Windows machines, but I have extensive experience on Macs as well. Which way the wind is blowing depends on who you ask. One thing's for sure--don't look for a solution to carry you 10 years down the road. In about 2-3 years, you'll have to completely replace everything anyway, since the software and hardware will have improved so much. Look past the emotions run amok, and go with what suits your needs and the needs of the PIs the best. Someone will always be hurt because their OS was insulted. You'll get the same crap about power drills, too. We have a mixed department of Windows, Mac and Suns. There isn't much trouble transferring files between them using common formats and the network drives. Mac's ANSI table is different than Windows, so you may have to go to a very low common denominator sometimes--either way, you're in for a little reformatting. I was fascinated by VectorNTI for Windows, as were a lot of people here. However, since we get "free" access to GCG on the Pittsburgh Supercomputing Center, we went with that. GCG does have a WWW interface in the new version. Haven't tried it yet, since PSC doesn't have it up yet. They have a free demo, as do a number of other companies. Hope this helps. If you need a few URLs for demos, let me know, and I'll passa long what I've collected. rich --- --- --- -- -- -- --- --- --- Richard J. Dudley (rdudley+@pitt.edu) Research Specialist V Dept. of Cell Biology and Physiology University of Pittsburgh http://www.cbp.pitt.edu ---> search BIONET archives at http://www.bio.net <--- From owner-software@net.bio.net Thu Mar 04 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: plantscigroup@my-dejanews.com Newsgroups: bionet.software Subject: Re: Secondary Structure Prediction Date: Fri, 05 Mar 1999 13:59:57 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 28 Message-ID: <7boo0n$knj$1@nnrp1.dejanews.com> References: <7bm3fq$7d1$1@mserv2.dl.ac.uk> <7bmcpu$rhp@web3.tcd.ie> NNTP-Posting-Host: 194.42.228.93 X-Article-Creation-Date: Fri Mar 05 13:59:57 1999 GMT X-Http-User-Agent: Mozilla/4.5 [en] (Win98; U) X-Http-Proxy: 1.0 x5.dejanews.com:80 (Squid/1.1.22) for client 194.42.228.93 In article <7bmcpu$rhp@web3.tcd.ie>, tpwalsh@acer.gen.tcd.ie (Urmhumhan) wrote: > m.hirshberg@mole.bio.cam.ac.uk wrote: > >> > >>What are the best 2D predictors availible ? > >>I am both looking for general predictors and specialized, such as only > >>for helices, strands etc. > > > >there are many try for example > > > >Jpred on http://circinus.ebi.ac.uk:8081/ > > Two of the best are: > > PHD: http://www.embl-heidelberg.de/predictprotein/ppDoPred.html > > DSC: http://bonsai.lif.icnet.uk/bmm/dsc/ > The following server is supposedly the most accurate currently available: PSIPRED: http://globin.bio.warwick.ac.uk/psipred Gary Marcher -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Thu Mar 04 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: charliejazz@my-dejanews.com Newsgroups: bionet.software Subject: Computer modeling position in Austin, Texas Date: Fri, 05 Mar 1999 20:09:50 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 63 Message-ID: <7bpdm5$95b$1@nnrp1.dejanews.com> NNTP-Posting-Host: 205.238.178.83 X-Article-Creation-Date: Fri Mar 05 20:09:50 1999 GMT X-Http-User-Agent: Mozilla/4.5 [en] (Win95; I) X-Http-Proxy: 1.0 x3.dejanews.com:80 (Squid/1.1.22) for client 205.238.178.83 To be upfront and honest, I am looking for someone who can perform topological geometry for a natural resources project. The money is good (high five figures to low six figure) and the locale is great (Austin,Texas). Please pass this around to those you think might be interested. Email me at: charliejazz@yahoo.com. I will ask forgiveness now for possibly violating the format of this user group. Here is the profile: Geometry Modeling Software Engineer Develop new model preparation and meshing capability for a reservoir simulator. This smulator is a new-technology, 4D (space-time) finite element analysis-based oil reservoir simulator for the petroleum industry. Key features of the simulator include automatic mesh generation, and automatic mesh adaption in 4D. Technical areas for this position are in FEA pre-processing, including: midsurface generation, model idealization, topology simplification, geometry repair, geometry meshing, assembly meshing and stitching. This person will interact with application engineers and customers to understand end user requirements. Then functional and design specifications will be developed and the projects coded and tested. The person will be expected to work independently and in teams, seeking help and cooperation where needed. Occasionally, the job can involve assisting customers in deploying the new technology. JOB REQUIREMENTS The qualified candidate will have a degree in Math, Physics or Engineering. An advanced degree or several years of large scale, engineering software development is required. The candidate must be proficient in C or C++ programming on large scale projects. Experience in rigorous software development methodology is required. Object Oriented methodology and Windows NT experience is a plus. The candidate must have experience developing mesh generation software. Applicant must understand the fundamentals of the use of FEA in structural, CFD or manufacturing analysis. Knowledge or experience in applying FEA to fluid dynamics problems is a real plus. Experience with commercial CAE packages is a plus. The candidate must have experience in at least one of the following areas: free form surface modeling, solid modeling, meshing, or some complex geometry and topology based application. Knowledge of CAD geometry, topology and numerical methods is required. Good oral and written communication skill in English is an absolute necessity. Other keywords: Computational fluid dynamics (CFD), Finite element analysis (FEA or FEM for F.E. Method), Computational grids, geometry meshing, Unstructured meshing. Thanks for your help. Let me know if anyone might be interested. Charlie Wirt -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Thu Mar 04 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.ecn.ou.edu!news.onenet.net!leto.backbone.ou.edu!news.ou.edu!not-for-mail From: "Benjamin Z. Goldsteen" Newsgroups: bionet.software Subject: Re: MolBio OS? Date: Fri, 05 Mar 1999 12:21:13 -0600 Organization: OMRF Lines: 33 Message-ID: <36E02099.6813AE26@zeta.omrf.ouhsc.edu> References: <36DB7DBD.51B54998@san.rr.com> <36DCBD46.F20C8628@san.rr.com> <78uib7.55l.ln@wpxx02.toxi.uni-wuerzburg.de> <36dd216b.1021900445@news.itn.is> <1kdjb7.p9n.ln@wpxx02.toxi.uni-wuerzburg.de> <7bjgkk$jgh$1@pegasus.csx.cam.ac.uk> Reply-To: benjamin-goldsteen@ouhsc.edu NNTP-Posting-Host: zeta.omrf.ouhsc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (X11; U; IRIX64 6.5 IP30) X-Accept-Language: en Justin Powell wrote: > > Our lab is planning to obtain a new computer for doing bioinformatics > work, currently we use our own macs and unix boxes belonging to the > department. We do mainly homology searches, protein motif searches, > function prediction and possibly some structural prediction. > It seems to me that the main determinant in our decision is is there any > software which we are likely to want to use in future which needs a unix > box to run on, or is everything available over the web these days? Just to throw myself into this discussion... I think UNIX systems offer the best software availability for what you want to do. In particular, SGI UNIX systems are very popular. You can break high-end software into three categories: -Those that support several UNIX and non-UNIX platforms -Those that support several UNIX platforms -Those that require SGI If you take an intersection of all the software you want to run, SGI is often the only viable platform. Your mileage may vary. My suggestion is to look at the software you want to run now and get that. I don't think waiting 6 months for the release of program X for platform Y is a good use of time. Time is worth more than money in research... Best -- Benjamin Z. Goldsteen Crystallography Program Oklahoma Medical Research Foundation 405 271 8954 / 405 271 7953 (FAX) From owner-software@net.bio.net Fri Mar 05 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!netnews.com!newsfeed.ecrc.net!newsfeed00.btx.dtag.de!newsmm00.btx.dtag.de!news.btx.dtag.de!not-for-mail From: RicoBaer@t-online.de (Mein Name) Newsgroups: bionet.software Subject: 3 Irre Typen und freie GAG-Programme Date: Sat, 6 Mar 1999 11:13:06 +0100 Lines: 11 Message-ID: <7bquke$g7o$1@news01.btx.dtag.de> Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news01.btx.dtag.de 920714702 16632 320085352551-0001 990306 10:05:02 X-Complaints-To: abuse@t-online.de X-Sender: 320085352551-0001@t-online.de X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Hallo Leute, lernt uns kennen ? 3 Irre Typen aus Salzgitter, außerdem Software-Gag-Programme für Win95/NT ein echtes "Muss" http://diedrei.home.pages.de Cu Euer 3m Team From owner-software@net.bio.net Sat Mar 06 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news-lond.gip.net!news.gsl.net!gip.net!iol!not-for-mail From: "Tony Tynan" Newsgroups: bionet.software Subject: Codelock programs Date: 7 Mar 1999 22:20:07 GMT Organization: Ireland On-Line Lines: 6 Message-ID: <01be68e9$742b0e40$0b307dc2@default> NNTP-Posting-Host: dialup-011.galway.iol.ie X-Newsreader: Microsoft Internet News 4.70.1161 Looking for apointer to sources iof information on codelocks, the kind that plug into the par port and meter program usage. I'm proposing to distribute an applicaton in tha form and would appreciate any help/or directions to an info source TT From owner-software@net.bio.net Sun Mar 07 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: Lchauvet74@aol.com Newsgroups: bionet.jobs.wanted,sci.materials,bionet.software,fl.jobs Subject: Bio/ Image processing / informatics : I need an internship! Date: Mon, 08 Mar 1999 18:56:24 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 53 Message-ID: <7c16gi$hl1$1@nnrp1.dejanews.com> NNTP-Posting-Host: 152.171.94.118 X-Article-Creation-Date: Mon Mar 08 18:56:24 1999 GMT X-Http-User-Agent: Mozilla/4.0 (compatible; MSIE 4.01; Windows 95) X-Http-Proxy: 1.1 x12.dejanews.com:80 (Squid/1.1.22) for client 152.171.94.118 Xref: biosci bionet.jobs.wanted:27714 bionet.software:23009 Laurent CHAUVET 14 rue Marcel Porte 38100 GRENOBLE, France  Tel : 33 4 7647 1478  Lchauvet74@aol.com Hello, I am a french student, and I am currently finishing an Advanced Professional Degree in Computer Science (Major Microscopic Imaging). and my course ends with a training period of at least three months (contract from the start of July until the end of September... but I can stay longer) in a company. From this course, I acquired: - an ability to quickly adapt myself to different programming languages, - a precise understanding of computer systems' functions, regarding software and hardware, - a good knowledge of the problems specific to software engineering (project managing, modeling, database building and managing). Also, I chose the Microscopy Imaging optional module which allowed me to have solid abilities regarding the differents systems for image acquisition (microscopy X-ray, confocal, electronic and optic) and image processing methods. This computing skills come in addition to a solid biological background: I have a Master degree Cells Biology and Physiology, giving me the possibility to analyse objectively biological problems. Interested for a long time in image analysis, I took on a temporary research fellowship in CNRS (Undergraduate level), regarding image analyses methods for the study of red blood cells deformation. I am currently working on the complete conception of a software for analysing image sequences using an algorithm of optical flow, within the framework of my course. Eventually, my professional aim is concerned with the conception of computing systems applied to life sciences (medical applications, structural biochemistry, biology, pharmacology). I am able to bring to you my skills as a trainee and thereby take profit of your experience in order to achieve my professional aim. If you have any opportunity for an internship in this field, please send me an e-mail (my address is Lchauvet74@aol.com) . If you wish to get more informations about my education, take a look at my resume on my Web site at this address : http://www.multimania.com/chauvetl/ Thanks, Laurent CHAUVET -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Sun Mar 07 22:00:00 1999 Path: biosci!CMMT.UBC.CA!francis From: francis@CMMT.UBC.CA Newsgroups: bionet.software Subject: Canadian Bioinformatics Workshop Series Date: 8 Mar 1999 10:52:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 47 Sender: daemon@net.bio.net Distribution: world Message-ID: <199903081843.KAA28321@monod.cmmt.ubc.ca> NNTP-Posting-Host: net.bio.net The Canadian Genetic Diseases Network and the Biotechnology Human Resources Council of Canada present a pilot series of practical computer-based workshops on "Bioinformatics" at the University of Calgary on August 2 - 14, 1999. With instructors: . Christopher Hogue, Mt. Sinai Hospital, Toronto . Francois Major, UniversitÇ de MontrÇal . Francis Ouellette, Centre for Mol. Medicine & Therapeutics, UBC . Christoph Sensen, Inst. for Marine Biosciences, NRC . David Wishart, University of Alberta >>>> WHO SHOULD APPLY People with an interest in bioinformatics with either a computer science/engineering or life science background. The workshop will give an introduction to the methodology and algorithms that underlie successful development and use of these tools. >>>> ADVANCED WORKSHOPS Participants will also be able to take three continuing one-week workshops on Genomics (Vancouver, January 2000), Proteomics (Toronto, May 2000) and Developing the Tools (Montreal, July 2000). For more information and to apply, please visit our website at: http://www.cmmt.ubc.ca/bioinformatics regards to all, francis -- | B.F. Francis Ouellette tel: (604) 875-3815 | | Director, Bioinformatics Core Facility fax: (604) 875-3800 | | Centre for Molecular Medicine and Therapeutics, UBC, Canada | | francis@cmmt.ubc.ca http://www.cmmt.ubc.ca | From owner-software@net.bio.net Sun Mar 07 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!news-peer.gip.net!news-lond.gip.net!news.gsl.net!gip.net!nntp.news.xara.net!xara.net!server6.netnews.ja.net!daresbury!not-for-mail From: "jayakumar" Newsgroups: bionet.software Subject: hi German research in BT Date: 8 Mar 1999 20:00:20 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 24 Message-ID: <7c1a8k$fbe$1@mserv2.dl.ac.uk> Reply-To: "jayakumar" NNTP-Posting-Host: mserv2.dl.ac.uk Mime-Version: 1.0 Original-To: "microbiology newsgroup" , "biosoftware on bionet" content-length: 942 Return-Path: X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 X-Priority: 3 Dear fellow netters Does anyone know of any Bacillus thuringiensis groups in Germany? or any website where I can search for such groups doing research in particular fields in Germany. I wish to do my DAAD fellowship sponsored short term project in one of these labs. Thanks in advance jakku **************************************************************************** ******************** R. Jayakumar, CSIR-SRF, School of Biotechnology, Madurai Kamaraj University, Madurai - 625021. India tel: +91-452-858464(hostel), 858471(ask for 374 to lab) fax: +91-452-859105 email: jakku@mrna.tn.nic.in \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\/////////// /////////////////////////////////////////////////////////////// VISIT MY WEBSITE AT http://members.tripod.com/~jakspage /////////////////////////////////////////////////////////////////\\\\\\\\\\\ \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ From owner-software@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!howland.erols.net!master.news.rcn.net!not-for-mail From: "Chris Baba" Newsgroups: bionet.software Subject: Great Software for the Lab Date: Tue, 9 Mar 1999 02:32:19 -0800 Lines: 16 Message-ID: <7c2iso$kb5$1@winter.news.rcn.net> X-Trace: fLN9OR+/GnJtQU0BpqMbe2V4PaqGn9odJzKJUU2NHVY= X-Complaints-To: abuse@rcn.com NNTP-Posting-Date: 9 Mar 1999 07:33:44 GMT X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 If you work in a lab as I do, you should try out the Chemical Calculator program which I wrote. Chemical Calculator (tm) is a shareware program designed for chemists, biologists and other scientific professionals. Its main purpose is to perform the calculations involved in the calculation of the amount of reagent to use when mixing up solutions. Chemical Calculator is a shareware program. You can use a fully functional version for 90 days and if you like it you can register it for $30.00. If you don't register Chemical Calculator you can still use a slightly disabled version for free after the 90 day trial period. Requires Windows 3.1 or later. More information is available on the Chemical Calculator Web Site: "http://www.erols.com/cbaba". The program can also be downloaded from there. From owner-software@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.tli.de!newsfeed.ecrc.net!news.net.uni-c.dk!not-for-mail From: "S.W. Rasmussen" Newsgroups: bionet.software Subject: Dnatools, revision 340 Date: Tue, 09 Mar 1999 22:02:42 +0000 Organization: UNI-C Lines: 14 Message-ID: <36E59A82.9A913FA3@crc.dk> NNTP-Posting-Host: 130.226.184.128 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.net.uni-c.dk 921013276 24356 130.226.184.128 (9 Mar 1999 21:01:16 GMT) X-Complaints-To: usenet@news.net.uni-c.dk NNTP-Posting-Date: 9 Mar 1999 21:01:16 GMT X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en New revision of DNATools is available at http://www.crc.dk/phys/A01B04_dnatools.htm Regards Soeren -- Soeren W. Rasmussen, Dr. scient. Department of Physiology Carlsberg Laboratory Copenhagen, Denmark swr@crc.dk, http://www.crc.dk/phys From owner-software@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!rutgers!nntp.upenn.edu!newsserver.jvnc.net!198.138.0.5!newshub.northeast.verio.net!newsfeed1.swip.net!swipnet!news.algonet.se!algonet!newsfeed.ecrc.net!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: SRock1158@aol.com Newsgroups: bionet.software Subject: per request Date: 9 Mar 1999 07:47:14 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 35 Message-ID: <7c2jm2$7aq$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk content-length: 697 Return-Path: Apparently-To: INTERNATIONAL DRIVER'S LICENSE Need a new driver's license? Too many points or other trouble? Want a license that can never be suspended or revoked? Want ID for nightclubs or hotel check-in? Avoid tickets, fines, and mandatory driver's education. Protect your privacy, and hide your identity. The United Nations gave you the privilege to drive freely throughout the world! (Convention on International Road Traffic of September 19, 1949 & World Court Decision, The Hague, Netherlands, January 21, 1958) Take advantage of your rights. Order a valid International Driver's License that can never be suspended or revoked. Confidentiality assured. CALL NOW!!! 1-937-586-9313 From owner-software@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed4.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.corridex.com!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: "jayakumar" Newsgroups: bionet.software Subject: a virus warning from me... Date: 9 Mar 1999 14:39:40 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 35 Message-ID: <7c3brc$k2m$1@mserv2.dl.ac.uk> Reply-To: "jayakumar" NNTP-Posting-Host: mserv2.dl.ac.uk Mime-Version: 1.0 Original-To: "microbiology newsgroup" , "biosoftware on bionet" content-length: 1656 Return-Path: X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 X-Priority: 3 Dear Users some of my mails had a Happy99.exe virus attached to it. I spotted it in my system yesterday and have exterminated it. I apologise if anybody got infected by it. The virus seemed to have got into my computer on 3/6/99 through a mail from the bionet newsgroup. This virus is a harmless one and does not do anything to your system. All users please check up your win95 systems. You need to delete the wsock32.dll file in your windows/system directory and rename the file wsock32.ska to wsock32.dll. The virus creates the wsock32.ska file. Then delete the file ska.exe from your computer. Probably it resides in the windows directory. The Happy99.exe has to be deleted too from the system. To protect your computer from re-infection you need just to set Read-Only attribute for the WSOCK32.DLL file. The worm does not pay attention to Read-Only mode, and fails to patch the file. This trick was discovered by Peter Szor at DataFellows http://www.datafellows.com. Sincerely jayakumar **************************************************************************** ******************** R. Jayakumar, CSIR-SRF, School of Biotechnology, Madurai Kamaraj University, Madurai - 625021. India tel: +91-452-858464(hostel), 858471(ask for 374 to lab) fax: +91-452-859105 email: jakku@mrna.tn.nic.in \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\/////////// /////////////////////////////////////////////////////////////// VISIT MY WEBSITE AT http://members.tripod.com/~jakspage /////////////////////////////////////////////////////////////////\\\\\\\\\\\ \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ From owner-software@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!washdc3-snf1!news.gtei.net!icet.net.nih.gov!news From: Jonathan Epstein Newsgroups: bionet.software Subject: publication quality alignments w/Motifs? Date: Tue, 09 Mar 1999 09:48:24 -0500 Organization: National Institutes of Health Lines: 22 Message-ID: <36E534B7.ACAB0E8D@nih.gov> NNTP-Posting-Host: 137.187.221.54 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (Win95; I) Hi, What do people out there use for producing publication-quality multiple alignments? In particular, I need to highlight some Motifs, and also should some discontinuity in some of the sequences, where I don't want to show hundreds of residues of uninteresting sequence. I have a PC on my desk, and have access to numerous Unix hosts, including one using GCG. In a pinch, I can use a Mac running MacVector. I need to get these diagrams out quickly, so am especially interested in freeware and/or time-bombed demos. I understand that Vector NTI is pretty well thought of these days for Windoze users. Does the demo version have the sorts of capabilities which I mention? TIA, - Jonathan From owner-software@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!198.82.160.249!solaris.cc.vt.edu!news.vt.edu!enya.fciencias.unam.mx!not-for-mail From: Lorenzo Segovia Newsgroups: bionet.software Subject: Re: BLAST output Date: Tue, 09 Mar 1999 09:47:14 -0600 Organization: Instituto de =?iso-8859-1?Q?Biotecnolog=EDa?= Lines: 39 Message-ID: <36E54282.FC99B460@ibt.unam.mx> References: <36E4FC1D.3B6@delete.this.bbsrc.ac.uk> NNTP-Posting-Host: burra.ceingebi.unam.mx Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------A7D560C07C7045337D512A8E" X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en This is a multi-part message in MIME format. --------------A7D560C07C7045337D512A8E Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, You should try MView. It is an extremely flexible interface once you get the hang of it. You can parse search outputs in very many different ways. http://mathbio.nimr.mrc.ac.uk/nbrown/mview/ Cheers, Lorenzo --------------A7D560C07C7045337D512A8E Content-Type: text/x-vcard; charset=us-ascii; name="lorenzo.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Lorenzo Segovia Content-Disposition: attachment; filename="lorenzo.vcf" begin:vcard n:Segovia;Lorenzo tel;fax:+52(73)172388 tel;work:+52(73)291862 or +52(73)291605 x-mozilla-html:FALSE org:Instituto de Biotecnología UNAM;DRMB adr:;;Apdo Post 510-3 ;Cuernavaca;Morelos;62250;Mexico version:2.1 email;internet:lorenzo@ibt.unam.mx x-mozilla-cpt:;-9024 fn:Lorenzo Segovia end:vcard --------------A7D560C07C7045337D512A8E-- From owner-software@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!newsfeed.nacamar.de!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!is.bbsrc.ac.uk!news From: michael.baron@delete.this.bbsrc.ac.uk Newsgroups: bionet.software Subject: BLAST output Date: Tue, 09 Mar 1999 10:46:53 +0000 Organization: BBSRC Biotechnology and Biological Sciences Research Council Lines: 23 Message-ID: <36E4FC1D.3B6@delete.this.bbsrc.ac.uk> NNTP-Posting-Host: pc0288.avri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Dear all, what programs exist for parsing or analysing the output from a BALST/FASTA search? I have found BOB, MacBOB and Visual BLAST (which are a great help). I would be particularly interested in a program that can help me to take all or a subset of the matches easily into a single multiple alignment. Thanks for any information or pointers, Michael *+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+ Michael D. Baron Ph.D. (michael.baron@bbsrc.ac.uk) Senior Research Scientist Institute for Animal Health Ash Road, Pirbright, Surrey, U.K. From owner-software@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newspeer.monmouth.com!easynet-fr!ciril.fr!univ-lille1.fr!u-strasbg.fr!news From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: images for bio softwares needed Date: 9 Mar 1999 10:11:57 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 11 Message-ID: <7c2s5d$2cd@news.u-strasbg.fr> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 1.0b.0 Mail-Copies-To: never Sorry, but I'm not able to find a site with icons and other presentation images for biology softwares. Any hint? Thanks to all. François. -- François Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France From owner-software@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!easynet-fr!ciril.fr!u-strasbg.fr!news From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: publication quality alignments w/Motifs? Date: 9 Mar 1999 15:25:38 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 47 Message-ID: <7c3ehi$3nh@news.u-strasbg.fr> References: <36E534B7.ACAB0E8D@nih.gov> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 1.0b.0 Mail-Copies-To: never In article <36E534B7.ACAB0E8D@nih.gov>, Jonathan Epstein writes: > Hi, > > What do people out there use for producing publication-quality multiple > alignments? alscript. > In particular, I need to highlight some Motifs, and also should some > discontinuity in some of the sequences, where I don't want to show > hundreds of residues of uninteresting sequence. I'm editing the .blc before running alscript to remove unwanted sequences and add "". You can find an example in : Jeanmougin F, Wurtz JM, LeDouarin B, Chambon P, Losson R The bromodomain revisited Trends Biochem Sci 1997;Vol 22, Iss 5:151-153 There waas a GUI for alscript but I prefer "vi" or writing the suitable script. Ho, yes, it's scripting, but it does what you attempt to (WYGIWYG). > I have a PC on my desk, and have access to numerous Unix hosts, > including one using GCG. In a pinch, I can use a Mac running MacVector. alscript produces high quality postscript output. > I need to get these diagrams out quickly, so am especially interested in > freeware and/or time-bombed demos. should be fast, just check alscript home page. > I understand that Vector NTI is pretty well thought of these days for > Windoze users. Does the demo version have the sorts of capabilities > which I mention? Dono. François. -- François Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France From owner-software@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!ODEE.COM!odee From: odee@ODEE.COM (odee) Newsgroups: bionet.software Subject: odee Date: 8 Mar 1999 20:57:20 -0800 Organization: odee Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <36E3DCB3.2611B620@odee.com> Reply-To: odee@odee.com NNTP-Posting-Host: net.bio.net Come and see us at www.odee.com, mail us we can help you!!!!! From owner-software@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!xmission!nntp.csuchico.edu!cscnews.csc.calpoly.edu!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software Subject: Re: Local BLAST server - any experience on dual/quad Intel - Linux platforms Date: 8 Mar 1999 20:18:51 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 51 Message-ID: <7c1bbb$2vd@gap.cco.caltech.edu> References: <36DD77A4.A62F9B42@uci.edu> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu In article <36DD77A4.A62F9B42@uci.edu>, Harry Mangalam writes: >Hi - I've been asked to eval setting up a local BLAST server. For >compatibility with other requirements, the OS will be Linux, unless >someone can give me extremely good reasons not to. > >I'm considering using a dual Pentium II/Celeron, unless I can get >feedback that BLAST does not work well on such a system, in which case >we would run either a uni-PII/Celeron or if more $ can be scraped up, an >Alpha (but having experience with Linux/Alpha, I know some of the >problems with that approach). > >So, does anyone out there have experience with BLAST on an SMP Intel box >(dual or quad (PPro or Xeon - I know that PII's can't go there) and if >so, on what kernel and what were the gotchas? We've BLAST locally on a Dual PII 400 in a machine we got from VAResearch. The kernel is close to RedHat 5.1. VAR put in some stuff to support the U2W drives, which were bleeding edge technology at the time we bought it. There is a thread parameter for BLASTALL, so it at least claims that it can use more than one processor at a time, but the PIIs can only go to dual processor in any case. > >Also rec's on minimum memory for maximum efficiency would be >appreciated. Lots. Running a query just against Genpept I've seen the blast process go over 128 Mb. Our server has 256 Mb in it, so I didn't try running two BLAST jobs at once, lest it bog down swapping virtual in and out. There may be a way to restrict memory safely, but blastall doesn't have an explicit switch for doing so. Linux caches what it can automatically. If this is to be a pure BLAST server, and you can buy enough memory to keep the desired databases entirely in memory, it will run much faster. The effect shows up for FASTA too, run it twice in a row against small database and it will be much faster the second time. Pure memory caching is feasible for Swiss-Prot, or maybe Genpept. Seems like a lot of money if you want Genbank to stay in memory though! The biggest job we've run on this box was 16000 BLASTP sequences against Genept, which took 9 days, two hours, and some change, to complete. We don't have the disks striped yet, that should speed things up a bit. Even so, the U2W disks are pretty fast. Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!not-for-mail From: AP-Pontis Newsgroups: bionet.software Subject: Announcing a new FREE online service Date: Tue, 09 Mar 1999 14:01:23 +0000 Organization: AP Pontis Biotechnology Lines: 57 Message-ID: <36E529B3.1E592958@ap-pontis.com> NNTP-Posting-Host: ind3.mrc-lmb.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en AP Pontis - The Heart of the Asia Pacific Biotechnology Industry ---------------------------------------------------------------- Announcing a new FREE online service We are an independent online service having a mission to promote biotechnology research in the Asia Pacific region. It is absolutely FREE! Make it your indispensible tool; become part of it! http://www.ap-pontis.com ##### Featured content:- ##### Looking for a research collaborator? Applying for research funding? We offer this unique service to match research supply and demand. A comprehensive listing of biotechnology jobs available in the Asia Pacific region. Employment advertisements are welcome. Announcing regional market and business news on the biotechnology industry. A must-see! Various links to online research tools, career websites, business tips, companies, institutions and scientists, information on events, patents, science, health and more! Come and visit AP Pontis today! http://www.ap-pontis.com ##### Highlights ##### PONTISMATCHING COLLABORATION: * Gene-based therapeutics company actively seeking partnerships with pharmaceutical and biotechnology companies. * Chinese drug research institute invites investment in newly patented anti-cancer drug. * University developed cold resistant grape. PONTIS JOBMARKET: * Group leader (biochemist/molecular pharmacologist) in Singapore. * Product specialists required in a leading pharmaceutical company, Malaysia. * Technology analyst(s) in a technology information programme, China. PONTIS MARKETNEWS: * S$80 Million New Facility to Enhance Glaxo Wellcome's Capabilities of Manufacturing New Generation Medicines in Singapore. * Glaxo Wellcome & AMRAD ICT Form Alliance to Treat Hepatitis B. * New System for DNA Chip Technology. * AMRAD and Ludwig Institute Allied with Baxter Healthcare to develop new therapy for ischaemic heart disease. http://www.ap-pontis.com From owner-software@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!NBRF.GEORGETOWN.EDU!huang From: huang@NBRF.GEORGETOWN.EDU (Hongzhan Huang) Newsgroups: bionet.software Subject: Re:BLAST output Date: 9 Mar 1999 07:33:54 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 66 Sender: daemon@net.bio.net Distribution: world Message-ID: <36E53D35.43730674@nbrf.georgetown.edu> NNTP-Posting-Host: net.bio.net Dear Dr. Baron, If you are working with protein sequences, our program could help you. We have developed a search program that provide a multiple alignment for selected matches from BLAST output. This search program is called PIR Annotation-Sorted Search (PASS). It searches the PIR-International Protein Sequence Database and display the top BLAST matches (up to100) with annotation ( Superfamily, family, Species, Taxonamic. group and Keywords). Full-length alignments are available. You may then sort and display the results of your original search in different ways and view multiple alignments of sequences you select. The URL is http://pir.georgetown.edu/pirwww/search/pass.html. If you have any question on the program, please let us know. Also, please send your suggestion to us so that we can improve the program. With the best regards, Hongzhan Huang, Ph.D. Senior Bioinformatics Scientist Protein Information Resource 3900 Reservoir Rd., NW Washington, DC 20007, USA e-mail: huang@nbrf.georgetown.edu > Date: Tue, 09 Mar 1999 10:46:53 +0000 > From: michael.baron@delete.this.bbsrc.ac.uk > To: bio-soft@net.bio.net > Subject: BLAST output > > Dear all, > > what programs exist for parsing or analysing the output from a > BALST/FASTA search? I have found BOB, MacBOB and Visual BLAST (which are > a great help). I would be particularly interested in a program that can > help me to take all or a subset of the matches easily into a single > multiple alignment. > > Thanks for any information or pointers, > > Michael > > > *+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+ > > Michael D. Baron Ph.D. (michael.baron@bbsrc.ac.uk) > > Senior Research Scientist > Institute for Animal Health > Ash Road, > Pirbright, > Surrey, > U.K. > > From owner-software@net.bio.net Tue Mar 09 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!oleane!pasteur.fr!jussieu.fr!univ-angers.fr!not-for-mail From: Armel Le Bail Newsgroups: bionet.software,bionet.xtallography Subject: PATSEE Date: Tue, 09 Mar 1999 13:44:39 +0100 Organization: Universite du Maine - France Lines: 16 Message-ID: <36E517B6.1E43742A@aviion.univ-lemans.fr> Reply-To: lebail@aviion.univ-lemans.fr NNTP-Posting-Host: pcb4122.univ-lemans.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [fr] (Win95; I) X-Accept-Language: fr Xref: biosci bionet.software:23024 bionet.xtallography:4645 Would it be possible to have access to more than one successful example as provided with the PATSEE package ? Any advice about, and experience with PATSEE is welcome (including data files). A summary of answers (if any) will be made. Thanks ! Armel Le Bail - Universite du Maine, Laboratoire des Fluorures, CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France http://www.cristal.org/ From owner-software@net.bio.net Tue Mar 09 22:00:00 1999 Path: biosci!CMMT.UBC.CA!francis From: francis@CMMT.UBC.CA Newsgroups: bionet.software Subject: Re: drawing a map Date: 10 Mar 1999 10:04:09 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: <199903101754.JAA05540@monod.cmmt.ubc.ca> NNTP-Posting-Host: net.bio.net > Given a 30 kb region of genomic DNA, and sequence start and stop info > on dozens of different exons that are of specific interest within this > sequence, what's the easiest way to draw a quick picture showing > visually just where all of these exons are, with labels? Dear Paula, to graphically represent your sequence data, I would recommend you give Sequin a try (it's free, so all you are risking is some of your time, although I know this can be a rare ressource for many). Sequin is a DNA submission tool, but you yan use it to view (and the idea is also to _review_before_you_submit) your data. Sequin is a network 'aware' tool (although it does work 'stand-alone' on your PC/Mac or unix box), and there is in it a very powerful style manager which allows you configure colors, labels, width of ligns and so on. You can download GenBank records, and see what they look like, make your own style sheet and, of course, put in your own data. Sequin is available from our friends at the NCBI: http:///www.ncbi.nlm.nih.gov/Sequin/ Where you will find help documentation, a quich startup guide, FAQ, dowwnload info and the ability to add yourself to the sequin notification e-mail list. There is also help available, at info@ncbi.nlm.nih.gov Because sequin is a sequence editinng tool, when you define new exons, or new exon bounderies (which sequin doess not currently do) the graphics is automatically updated -- it's actually a good idea to have a graphics window up, as well as a text view of the GBFF (GenBank flat file). I know there are quite a few sequin users at Baylor, so maybe there is some local expertise you draw on ... hope this helps, francis -- | B.F. Francis Ouellette tel: (604) 875-3815 | | Director, Bioinformatics Core Facility fax: (604) 875-3800 | | Centre for Molecular Medicine and Therapeutics, UBC, Canada | | francis@cmmt.ubc.ca http://www.cmmt.ubc.ca | > This is quite different from exon prediction. We already know where > the sequences of interest are - we need a summary to which we can > easily refer. Drawing a map either by hand or with the computational > tools I know takes a huge amount of time, though. Is there an existing > tool to make it quick and easy? > > ________________________________________________________________________ > Paula E. Burch, Ph.D. Molecular Biology Computation Resource > Baylor College of Medicine, BCMM M220 voice: 713.798.6023 > One Baylor Plaza, Houston, Texas 77030 fax: 713.798.4279 > http://mbcr.bcm.tmc.edu/pburch.html email: pburch@bcm.tmc.edu > > From owner-software@net.bio.net Tue Mar 09 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!intgwpad.nntp.telstra.net!news1.optus.net.au!optus!bunyip.cc.uq.edu.au!axis.scu.edu.au!rkota From: Raja Kota Newsgroups: bionet.software Subject: MapMaker Date: Wed, 10 Mar 1999 17:24:09 +1100 Organization: SCU Lines: 10 Message-ID: <100319991724096309%rkota@scu.edu.au> NNTP-Posting-Host: ip3956.scu.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: YA-NewsWatcher/3.1.8 Hi Netters, Can anyone tell me what's the best way to easily access Mapmarker exp/qtl from the web. Alternatively, can I download a version of Mapmaker which is compatible for running on a macintosh computer. Thanks in advance, Raja Raja From owner-software@net.bio.net Tue Mar 09 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!24.128.1.125!chnws03.mediaone.net!24.128.1.101!chnws05.ne.mediaone.net!24.128.16.7!lwnws01.ne.mediaone.net.POSTED!not-for-mail Message-ID: <36E680DB.E2A7489F@mediaone.net> From: Hemant Chikarmane X-Mailer: Mozilla 4.5 (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software Subject: Re: MapMaker References: <100319991724096309%rkota@scu.edu.au> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Lines: 11 Date: Wed, 10 Mar 1999 09:25:32 -0500 NNTP-Posting-Host: 24.128.204.200 X-Trace: lwnws01.ne.mediaone.net 921075810 24.128.204.200 (Wed, 10 Mar 1999 09:23:30 EDT) NNTP-Posting-Date: Wed, 10 Mar 1999 09:23:30 EDT Organization: Northeast Region--MediaOne Raja, The Mac version of Mapmaker is available from Scott Tingey of Dupont. Give me a day or so and I will dig up his email - it is most likely: svtingey@dupont.com Hemant Chikarmane Marine Biological Laboratory Woods Hole MA 02543 From owner-software@net.bio.net Tue Mar 09 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.msfc.nasa.gov!bcm.tmc.edu!news From: pburch@mbcr.bcm.tmc.edu (Paula Burch) Newsgroups: bionet.software Subject: drawing a map Date: 10 Mar 1999 16:49:14 GMT Organization: Baylor College of Medicine, Houston, Tx Lines: 16 Message-ID: <7c67qa$bg7@gazette.bcm.tmc.edu> NNTP-Posting-Host: roc.mbcr.bcm.tmc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 0.9.8 X-No-Archive: yes Given a 30 kb region of genomic DNA, and sequence start and stop info on dozens of different exons that are of specific interest within this sequence, what's the easiest way to draw a quick picture showing visually just where all of these exons are, with labels? This is quite different from exon prediction. We already know where the sequences of interest are - we need a summary to which we can easily refer. Drawing a map either by hand or with the computational tools I know takes a huge amount of time, though. Is there an existing tool to make it quick and easy? ________________________________________________________________________ Paula E. Burch, Ph.D. Molecular Biology Computation Resource Baylor College of Medicine, BCMM M220 voice: 713.798.6023 One Baylor Plaza, Houston, Texas 77030 fax: 713.798.4279 http://mbcr.bcm.tmc.edu/pburch.html email: pburch@bcm.tmc.edu From owner-software@net.bio.net Tue Mar 09 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: FoxeTopp@aol.com Newsgroups: bionet.software Subject: Strengthen your marrige or relationship Date: 10 Mar 1999 06:48:01 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 37 Message-ID: <7c54j1$kp1$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk content-length: 813 Return-Path: Apparently-To: ------------------------------------------------------------------------------ --------------------------- -Increase your sexual potential -Strengthen your marriage or relationship -Increase lust and romance -Better foreplay -Exercises anyone can do -Increase passion and desire -Be able to have sex more times a day -Satisfy your partners needs Its time to put futher enjoyment into your life, time is limited so use it to its full pleasure. Order our informational guide to Strengthen your marriage or relationship for our print value of $9.00. We will rush your guide to you within days of you receiving your payment. Ordering instructions are below. Order by mail send payment to: K.C. Smith 10 East Louisiana Evansville, IN 47711 Make sure to write your address twice to ensure delivery. From owner-software@net.bio.net Tue Mar 09 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.ucsc.edu!karplus From: karplus@cse.ucsc.edu (Kevin Karplus) Newsgroups: bionet.software Subject: Re: Secondary Structure Prediction Date: 10 Mar 1999 20:19:42 GMT Organization: UC Santa Cruz CS/CE Lines: 30 Message-ID: <7c6k4u$d8l@darkstar.ucsc.edu> References: <7bm3fq$7d1$1@mserv2.dl.ac.uk> <7bmcpu$rhp@web3.tcd.ie> <7boo0n$knj$1@nnrp1.dejanews.com> NNTP-Posting-Host: purr.cse.ucsc.edu X-newsreader: xrn 9.00 Originator: karplus@cse.ucsc.edu In article <7boo0n$knj$1@nnrp1.dejanews.com>, plantscigroup@my-dejanews.com writes: |> The following server is supposedly the most accurate currently available: |> |> PSIPRED: http://globin.bio.warwick.ac.uk/psipred |> |> Gary Marcher At the CASP3 contest last December, two secondary-structure predictors stood out as superior to the rest---PSIPRED was the best. The second-best was a predictor that Christian Barrett and I wrote that we have not released (it was a class project for Christian and a recreational project for me). We hope to release a real secondary-structure predictor later this year, combining Christian's work with two other predictors we've been developing at UCSC. Until that comes on-line, PSIPRED is definitely your best bet. -- Kevin Karplus karplus@cse.ucsc.edu http://www.cse.ucsc.edu/~karplus life member (LAB, Adventure Cycling, American Youth Hostels) Effective Cycling Instructor #218-ck -- Kevin Karplus karplus@cse.ucsc.edu http://www.cse.ucsc.edu/~karplus life member (LAB, Adventure Cycling, American Youth Hostels) Effective Cycling Instructor #218-ck From owner-software@net.bio.net Tue Mar 09 22:00:00 1999 Path: biosci!sanger.ac.uk!solovyev From: solovyev@sanger.ac.uk ("Victor Solovyev") Newsgroups: bionet.software Subject: New gene-finding program FGENES, FGENESH .. installed at BCM Date: 10 Mar 1999 10:38:48 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <9903101833.ZM23574@octane> NNTP-Posting-Host: net.bio.net New gene-finding program FGENES, FGENESH, FGENESP, BESTORF are installed at the Baylor Collge of Medicine (USA) Search Launcher WEB server http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html The programs can analyze genomic sequence up to 1.5 MB and file with the sequence in FASTA format can be loaded Go to: * BCM Gene Finder * BCM protein secondary structure prediction Programs have been developed by Victor Solovyev and Asaf Salamov for multiple gene/best ORF prediction in human/plant genomic DNA Gene-finding WEB page: http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html Secondary structure prediction and prosite patterm search WEB: http://dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.html The programs also can be run at http://genomic.sanger.ac.uk/ of our Computational Genomic Group WEB server -- Victor Solovyev The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK Email: solovyev@sanger.ac.uk http://genomic.sanger.ac.uk Phone: 44-1223-494799 FAX: 44-1223-494919 From owner-software@net.bio.net Tue Mar 09 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!sunqbc.risq.qc.ca!news.uow.edu.au!news.usyd.edu.au!sunb.ocs.mq.edu.au!apaf From: phains@proteome.org.au (Peter Hains) Newsgroups: bionet.software Subject: Re: publication quality alignments w/Motifs? Date: Wed, 10 Mar 1999 21:40:57 GMT Organization: Australian Proteome Analysis Facility Lines: 46 Message-ID: <7c6lcm$5c4$1@sunb.ocs.mq.edu.au> References: <36E534B7.ACAB0E8D@nih.gov> NNTP-Posting-Host: godzilla.proteome.org.au X-Newsreader: News Xpress 2.01 Jonathan, I can thoroughly recommend Genedoc for Win3.11 or Win9X available at www.cris.com/~ketchup/genedoc.shtml Peter In article <36E534B7.ACAB0E8D@nih.gov>, Jonathan Epstein wrote: >Hi, > >What do people out there use for producing publication-quality multiple >alignments? > >In particular, I need to highlight some Motifs, and also should some >discontinuity in some of the sequences, where I don't want to show >hundreds of residues of uninteresting sequence. > >I have a PC on my desk, and have access to numerous Unix hosts, >including one using GCG. In a pinch, I can use a Mac running MacVector. > >I need to get these diagrams out quickly, so am especially interested in >freeware and/or time-bombed demos. > >I understand that Vector NTI is pretty well thought of these days for >Windoze users. Does the demo version have the sorts of capabilities >which I mention? > >TIA, > >- Jonathan I'm afraid I don't have a clever saying to put here. Remove NOSPAM to e-mail me. Peter Hains (PhD) Ph. +61 2 9850 6216 Australian Proteome Analysis Facility Fax. +61 2 9850 6200 Level 4 Building F7B Macquarie University, Sydney 2109 From owner-software@net.bio.net Tue Mar 09 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!newsfeed.nacamar.de!frankfurt.de.uu.net!news.uni-stuttgart.de!news.belwue.de!news-stu1.dfn.de!news-mue1.dfn.de!news.gsf.de!news From: "K. Quandt" Newsgroups: bionet.software Subject: DiAlign available online Date: Wed, 10 Mar 1999 15:15:57 +0100 Organization: GSF Forschungszentrum Lines: 30 Message-ID: <36E67E9C.446B@gsf.de> NNTP-Posting-Host: savannah.gsf.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V4.0 alpha) We would like to announce the availability of an online version of the multiple alignment program DiAlign on the Genomatix web server at http://genomatix.gsf.de/cgi-bin/dialign/dialign.pl DiAlign relies on comparing whole segments of DNA or protein sequences instead of comparing single residues. Pairwise as well as multiple alignments are constructed from gapfree pairs of segments (so-called `diagonals'). DiAlign does not use any gap penalty, thus avoiding this critical parameter. Consequently, the program is able to detect isolated local homologies that can not be detected by standard multiple alignment methods. New features include a new user interface and an optional color-coding of the alignment output. The use of this software is free for non-commercial use! Users with a commercial affiliation interested in using or obtaining DiAlign please contact Genomatix Software at genomatix@gsf.de . -- Kerstin Quandt quandt@gsf.de Genomatix Software GmbH http://genomatix.gsf.de Karlstrasse 55 80333 Muenchen, Germany From owner-software@net.bio.net Wed Mar 10 22:00:00 1999 Path: biosci!agate!dog.ee.lbl.gov!newsfeed.berkeley.edu!news-peer1.sprintlink.net!news-in-east1.sprintlink.net!news.sprintlink.net!itssrv1.ucsf.edu!macmac-2.ucsf.edu!user From: bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD) Newsgroups: bionet.software Subject: Re: drawing a map Date: Wed, 10 Mar 1999 20:04:57 -0700 Organization: University of California, San Francisco Lines: 23 Message-ID: References: <7c67qa$bg7@gazette.bcm.tmc.edu> NNTP-Posting-Host: macmac-2.ucsf.edu In article <7c67qa$bg7@gazette.bcm.tmc.edu>, pburch@mbcr.bcm.tmc.edu (Paula Burch) wrote: > Given a 30 kb region of genomic DNA, and sequence start and stop info > on dozens of different exons that are of specific interest within this > sequence, what's the easiest way to draw a quick picture showing > visually just where all of these exons are, with labels? > > This is quite different from exon prediction. We already know where > the sequences of interest are - we need a summary to which we can > easily refer. Drawing a map either by hand or with the computational > tools I know takes a huge amount of time, though. Is there an existing > tool to make it quick and easy? I don't know if this is quite what you mean but when I had to do this I used a plasmid drawing program in "linear" mode and used a "gene" or "insert" to represent each exon. Its been a while so I can't remember exactly which program I used. Bernard -- Bernard P. Murray, PhD Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA From owner-software@net.bio.net Wed Mar 10 22:00:00 1999 Path: biosci!pravda.ucr.edu!not-for-mail From: Alan Williams Newsgroups: bionet.software Subject: GDE on Linux Date: 10 Mar 1999 23:33:57 GMT Organization: University of California, Riverside Lines: 24 Message-ID: <7c6vh5$9sr$2@pravda.ucr.edu> NNTP-Posting-Host: avocado.ucr.edu User-Agent: tin/pre-1.4-981002 ("Phobia") (UNIX) (Linux/2.0.34 (i586)) I have been setting up some molbio software on several linux machines and have several questions regarding GDE: First off, I am using GDE 2.2. I have noticed an anoying bug when cutting and pasting whole sequences. On the second cut the program crashes. Has anyone else encountered this bug? Any fixes? Less important: Has anyone put together some good .GDEmenus (and any necessary scripts) for interfacing to alscript, phylip, clustal, tacg, ... ? Any menu segments would be appreciated. What every I come up with in the end I will make available here. Thanks, Alan Williams ************************************************************************ Alan Williams (finger alan@avocado.ucr.edu for pgp public key) ------------------------------------------------------------------------ University of California, Riverside "Where observation is concerned, Dept. of Botany and Plant Sciences chance favors the prepared mind." Alan@Avocado.UCR.edu -- Louis Pasteur ************************************************************************ From owner-software@net.bio.net Wed Mar 10 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news-peer1.sprintlink.net!news-in-east1.sprintlink.net!news.sprintlink.net!news2.smatnet.net!news.sprintsvc.net!news.smatnet.net!uunet!ffx.uu.net!in4.uu.net!news.ici.net!not-for-mail From: "Hilton Evans" Newsgroups: bionet.software Subject: Molecular Mechanics Software Date: Thu, 11 Mar 1999 01:47:32 -0500 Organization: ChemPen Software Lines: 4 Message-ID: <7c7osl$r42$1@bashir.ici.net> Reply-To: "Hilton Evans" NNTP-Posting-Host: d-gnaps-75.ici.net Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 ChemPen3D for Win95/NT -- http://home.ici.net/~hfevans/chempen3d.htm Chemical Structure Drawing -- http://home.ici.net/~hfevans/chempen.htm Coming Summer 1999 -- ChemPen+NMR