From owner-software@net.bio.net Sat Aug 01 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!newspeer.monmouth.com!news.cs.utwente.nl!newsfeed.xs4all.nl!xs4all!not-for-mail From: "Sjaak" Newsgroups: bionet.software Subject: Powerpack 6.0i Date: Sun, 2 Aug 1998 10:03:41 +0200 Organization: XS4ALL, networking for the masses Lines: 5 Message-ID: <6q168s$joh$1@news2.xs4all.nl> NNTP-Posting-Host: dc2-isdn386.dial.xs4all.nl X-NNTP-Posting-Host: dc2-isdn386.dial.xs4all.nl [194.109.149.130] X-XS4ALL-Date: Sun, 02 Aug 1998 09:59:24 CEST X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Hi, Can anybody get me the new powerpack 6.0i for a Teles isdn adapter? From owner-software@net.bio.net Sat Aug 01 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!island.idirect.com!newsfeed.gamma.ru!Gamma.RU!nntpgate.globalserve.net!209.90.128.12.MISMATCH!news.globalserve.net!not-for-mail From: "Danny Reda" Newsgroups: bionet.software Subject: New Plasmid Drawing Program! Date: Sun, 2 Aug 1998 11:05:53 -0400 Organization: GlobalServe Communications Inc. Lines: 12 Message-ID: <6q1vaq$t4$1@whisper.globalserve.net> NNTP-Posting-Host: dialin1809.toronto.globalserve.net X-Trace: whisper.globalserve.net 902070426 932 209.90.137.30 (2 Aug 1998 15:07:06 GMT) X-Complaints-To: abuse@globalserve.net NNTP-Posting-Date: 2 Aug 1998 15:07:06 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Introducing Redasoft Plasmid 1.0 - an exciting new software tool designed to help life scientists draw vector maps and perform DNA sequence analysis quickly and easily. Plasmid includes revolutionary new features such as an integrated web browser and the ability to instantly convert a Genbank file from the Internet into a fully labeled graphical vector map! We have just added a FREE and fully functional test version of Plasmid to our Web site. Visit www.redasoft.com to get your copy today! From owner-software@net.bio.net Sat Aug 01 23:00:00 1998 Path: biosci!ACCEFYN.ORG.CO!acad From: acad@ACCEFYN.ORG.CO (Alexander Garcia) Newsgroups: bionet.software Subject: xwindows clinet Date: 2 Aug 1998 10:58:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <35C4A854.F282DE16@accefyn.org.co> Reply-To: acad@accefyn.org.co NNTP-Posting-Host: net.bio.net Where can I download a good freeware, shareware or evaluation copy of a xwindows client? thanks a lot in advance, cheers From owner-software@net.bio.net Sat Aug 01 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!206.229.87.25!news-peer.sprintlink.net!news-peer-east.sprintlink.net!news.sprintlink.net!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!duke.telepac.pt!news.telepac.pt!not-for-mail From: "C.A.C.C." Newsgroups: bionet.software Subject: Read this ! Date: Sun, 2 Aug 1998 18:34:09 +0100 Lines: 33 Message-ID: <6q27fg$hi9$1@duke.telepac.pt> NNTP-Posting-Host: 194.65.223.36 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 This is an excitting new service that can change your life for the better ! : :The Blue Rabbit has been scanning the Internet for the last 2 years and has discovered and purchased the publishing rights to hundreds of reports , publications and great software titles . He has now compiled them into an online library and along with a list of secret links he has created a website that he calls THE BLUE RABBIT E-LIBRARY . 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Sign-Up now in : http://www.uksecrets.co.uk/bluerabbit/library/7771 From owner-software@net.bio.net Sat Aug 01 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!cpk-news-hub1.bbnplanet.com!chicago-news-feed2.bbnplanet.com!news.bbnplanet.com!news.itis.com!aiyar.dyn.ml.org!aiyar From: aiyar@aiyar.dyn.ml.org (Ashok Aiyar) Newsgroups: bionet.software Subject: Re: xwindows clinet Date: 2 Aug 1998 19:52:36 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 18 Distribution: world Message-ID: References: <35C4A854.F282DE16@accefyn.org.co> Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: mptc1-cas-22.dial.midplains.net X-Newsreader: slrn (0.9.5.1 UNIX) On 2 Aug 1998 10:58:18 -0700, Alexander Garcia wrote: >Where can I download a good freeware, shareware or evaluation copy of a >xwindows client? thanks a lot in advance, cheers I think you are looking for an Xserver, and not an Xclient (Xclients display their output on an Xserver). You don't state what platform you need an Xserver for; however MicroImages provide free Xservers for MacOS (m68k and PPC), as well as Win32 (Intel). These are available from: http://www.microimages.com/freestuf/mix/download.htm Later, Ashok -- Ashok Aiyar, Ph.D. McArdle Laboratory for Cancer Research aiyar@ebv.oncology.wisc.edu From owner-software@net.bio.net Sun Aug 02 23:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: G.Vidarsson@Pobox.accu.uu.nl Newsgroups: bionet.software Subject: ELISA program, Titri Date: Mon, 03 Aug 1998 09:36:53 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 28 Message-ID: <6q40bl$fba$1@nnrp1.dejanews.com> NNTP-Posting-Host: 131.211.169.75 X-Article-Creation-Date: Mon Aug 03 09:36:53 1998 GMT X-Http-User-Agent: Mozilla/4.05 [en] (Win95; I) I have confirmed that the distribution file of the 32 bit version of the ELISA reader program TITRI is damaged. I apologize for this. For technical reasons (I can not reach my computer as I am on a vacation), I am unable to fix this until next week. In the mean time, you can download the 16 bit version which is identical in function as the 32 bit version at http://members.tripod.com/~gestur/programs/titri.htm Sincerely, Gestur Vidarsson, Department of Immunology, University Hospital Utrecht (AZU) Rm G04.614 Heidelberglaan 100 3584 CX Utrecht The Netherlands TEL +31 (0)30 253 3925 / 250 6520 FAX +31 (0)30 250 5449 -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-software@net.bio.net Sun Aug 02 23:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!howland.erols.net!newsfeed.nacamar.de!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!gwilliam From: gwilliam@hgmp.mrc.ac.uk (Gary Williams) Newsgroups: bionet.software Subject: Re: bioinformatics information Date: 3 Aug 1998 09:29:48 GMT Organization: UK HGMP Resource Centre Lines: 11 Message-ID: <6q3vuc$5t9$1@niobium.hgmp.mrc.ac.uk> References: <35BA140B.EDC8814E@ncl.ac.uk> NNTP-Posting-Host: neptunium.hgmp.mrc.ac.uk In article <35BA140B.EDC8814E@ncl.ac.uk>, Francisco Pereira wrote: >Hello > >Could anybody tell me a good URL with links to Bioinformatics >information ? Try: http://www.hgmp.mrc.ac.uk/GenomeWeb/docs-bioinf-course-info.html From owner-software@net.bio.net Sun Aug 02 23:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news-backup-west.sprintlink.net!news.sprintlink.net!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: josephryan@yahoo.com Newsgroups: bionet.software Subject: Re: BP2.pm for NCBI Blast 2? Date: Mon, 03 Aug 1998 22:41:04 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 49 Message-ID: <6q5ea0$ek9$1@nnrp1.dejanews.com> References: <35C5A8BB.5A212216@lilly.com> NNTP-Posting-Host: 165.112.191.175 Keywords: NCBI BLAST blastall parse perl To: kauffman_e_wayne_ii@lilly.com X-Article-Creation-Date: Mon Aug 03 22:41:04 1998 GMT X-Http-User-Agent: Mozilla/4.05 [en] (X11; U; Linux 2.0.32 i586) > Has anyone modified Ian Korf's BP2.pm to support NCBI BLAST v2.0x Wayne, NHGRI::Blastall.pm is not a modification of Ian Korf's code but the functionality is similar. I have included the Release announcement. NHGRI::Blastall.pm is Alpha software but should be helpful. If you have questions, comments, or suggestions send me mail to @ jfryan^nhgri.nih.gov --------------------------------------------------------------------- This message is to announce the first public alpha release of NHGRI::Blastall.pm. Docs and other info available at http://genome.nhgri.nih.gov/blastall/. Feedback is appreciated. This module is designed to run NCBI's standalone BLAST or initialize existing BLAST reports and provide access for various elements of the report. Blastall.pm also provides a filter method which allows for filtering against an ecoli, repeat or any other database. The motivation behind NHGRI::Blastall.pm was for it to work with the forthcoming version of our NHGRI-WebBLAST http://genome.nhgri.nih.gov/webblast/. NHGRI::Blastall.pm and NHGRI-WebBLAST are public domain software. ------------------------------------------------------------------------ In article <35C5A8BB.5A212216@lilly.com>, Wayne Kauffman wrote: > BLAST parsing time.... > > Has anyone modified Ian Korf's BP2.pm to support NCBI BLAST v2.0x and is > the modified BP2 code available? I am trying not to re-invent the wheel > if it has been already accomplished. :-) > > Wayne Kauffman > Eli Lilly and Company > Lilly Corporate Center, MS0444 > Indianapolis, IN 46285 > > 317-276-9750 > wayne@lilly.com > > -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-software@net.bio.net Sun Aug 02 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!news.iquest.net!cronkite.d48.lilly.com!not-for-mail From: Wayne Kauffman Newsgroups: bionet.software Subject: BP2.pm for NCBI Blast 2? Date: Mon, 03 Aug 1998 07:10:35 -0500 Organization: Eli Lilly and Company Lines: 15 Message-ID: <35C5A8BB.5A212216@lilly.com> NNTP-Posting-Host: guru2.d50.lilly.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; U) BLAST parsing time.... Has anyone modified Ian Korf's BP2.pm to support NCBI BLAST v2.0x and is the modified BP2 code available? I am trying not to re-invent the wheel if it has been already accomplished. :-) Wayne Kauffman Eli Lilly and Company Lilly Corporate Center, MS0444 Indianapolis, IN 46285 317-276-9750 wayne@lilly.com From owner-software@net.bio.net Sun Aug 02 23:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!209.95.128.196!news-nyc.telia.net!chippy.visi.com!news-out.visi.com!news.state.mn.us!news1.mr.net!news.mr.net!not-for-mail From: "KingSky" Newsgroups: alt.binaries.dominion.freeware,alt.binaries.win95-graphic,alt.comp.freeware,alt.comp.freeware.gdp,alt.comp.software.financial,alt.comp.software.tools,bionet.software,biz.comp.software,biz.comp.software.demos,comp.os.ms-windows.apps.compatibility.win95,com Subject: Check out the FREEWARE!! Date: Mon, 3 Aug 1998 05:13:22 -0400 Organization: [poster's organization not specified] Lines: 12 Message-ID: <6q5cqp$qgn$1@news3.mr.net> NNTP-Posting-Host: aa118.ips.paulbunyan.net X-Newsreader: Microsoft Outlook Express 4.72.3115.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Come and check out my fresh, constantly updated freeware page at Http://freeloader.simplenet.com/index.html! It has loads of software for Windows 95/98 and NT. All the newest browsers, multimedia, plug-ins, business programs, graphics and internet utilities. Visit often, and Load Up On FreeWare! Thanks for Reading! WebMaster http://freeloader.simplenet.com/index.html Load up on FreeWare!! From owner-software@net.bio.net Sun Aug 02 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!206.229.87.25!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news.sprintlink.net!207.69.200.14!firehose.mindspring.net!cssun.mathcs.emory.edu!cronkite.cc.uga.edu!twopaths From: russell@dogwood.botany.uga.edu (Russell Malmberg) Newsgroups: bionet.software Subject: Trbls - timed blast search utility - is available for win95/NT4 Date: Mon, 03 Aug 1998 17:19:54 GMT Organization: Botany Department, University of Georgia Lines: 48 Message-ID: <6q4rf7$smf$1@cronkite.cc.uga.edu> NNTP-Posting-Host: twopaths.botany.uga.edu X-Newsreader: News Xpress 2.01 There is a new version of Trbls (version 0.55), my Timed-Run-Blast -Search accessory program for Windows 95 or NT4. Versions are available for both intel and alpha CPUs. Trbls is a utility designed to partially automate some aspects of routine blast searches. The user can select multiple sequences, set their blast search parameters, and then schedule runs for some time. You might set your favorite sequences to be run every Saturday at 4 AM, for example. Trbls will perform both regular and gapped blast searches, and it will return output in HTML format, which leads to direct links to the sequences of interest. I wanted to have a timed program like Trbls for my own blast searches, so I wrote this, and am distributing it in the hope that others will find it useful. Trbls uses slightly modified two blast clients from NCBI to actually perform the search (blastcl2 and blastcl3). All the credit for the blast functionality should thus go to NCBI (with particular thanks from me to Tom Madden). You can get Trbls by entering these references directly into your web browser, or by going to my software page. for Windows 95 or Windows NT4 (intel processor): http://www.botany.uga.edu/malmberg/programs/Trbls-intel.zip for Windows NT4 (alpha processor): http://www.botany.uga.edu/malmberg/programs/Trbls-alpha.zip my software web page page: http://dogwood.botany.uga.edu/malmberg/software.html What to do when you get it: -- unzip in some useful directory (C:\Program Files\Trbls, for example) -- follow the directions in Setup.txt file. -- read the "getting started" section of the Trbls.hlp file. sample input and output files are included. Please send me your comments on the program, the help file, or anything else about Trbls. ----- Russell L. Malmberg russell@dogwood.botany.uga.edu http://dogwood.botany.uga.edu/malmberg/ From owner-software@net.bio.net Sun Aug 02 23:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!newspump.monmouth.com!newspeer.monmouth.com!netnews.com!news2.euro.net!194.165.93.117.MISMATCH!newsfeed.wirehub.nl!news.wirehub.nl!not-for-mail From: lu.do@home.diva.nl (Lucas Noldus) Newsgroups: bionet.software Subject: Measuring Behavior '98: last chance to register Date: Mon, 03 Aug 1998 22:06:40 GMT Organization: Wirehub! Internet Lines: 34 Message-ID: <35c63464.58208892@news.diva.nl> NNTP-Posting-Host: 195.86.38.42 X-Newsreader: Forte Free Agent 1.11/32.235 MEASURING BEHAVIOR '98 2nd International Conference on Methods and Techniques in Behavioral Research Groningen, The Netherlands 18-21 August 1998 With this message we would like to remind you that it is still possible to register for Measuring Behavior '98. A few places are left for participation. The registration fee is NLG 600 (students: NLG 300). One Dutch guilder (NLG 1) equals approx. US$ 0,50. The conference website (http://www.noldus.com/events/mb98/mb98.htm) has been updated thoroughly and now also contains the full program with all oral presentations, posters and demonstrations. The site also has updated information about exhibitors of books, instruments and software. We hope to see you at Measuring Behavior '98! Wineke Schoo Chair Local Organizing Committee Measuring Behavior '98 Conference Secretariat P.O. Box 268 6700 AG Wageningen The Netherlands Phone: +31-317-497677 Fax: +31-317-424496 E-mail: mb98@noldus.nl Web: http://www.noldus.com/events/mb98/mb98.htm From owner-software@net.bio.net Mon Aug 03 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.nyu.edu!btnet-peer!btnet!dispose.news.demon.net!demon!delos!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: blast 1.4 "too short" for the size of genbank and embl Date: 4 Aug 1998 12:18:14 GMT Organization: University of Cambridge Message-ID: <6q6u66$j2v$1@pegasus.csx.cam.ac.uk> References: <6q6jrt$h8p$1@desdemone.pasteur.fr> NNTP-Posting-Host: mole.bio.cam.ac.uk Lines: 48 In article <6q6jrt$h8p$1@desdemone.pasteur.fr>, Catherine Letondal wrote: > >Hi, > >We maintain a copy of genbank (release + updates) as well as embl for >blast 1.4 searches. The problem is that these databases have reached a >size that exceeds a 32 bits integer capacity - and this version of blast is >mainly based on such types of integer (more exactly 31 bits, for the >integers are not unsigned). As a result, malloc of negative >numbers occur. > >Of course, we also have the blast 2 NCBI and Washington-Univ. versions. >We are aware that this version of blast is not maintained anymore at NCBI, but >we keep the "old" 1.4 version of blast for compatibility reasons >with blast output parsers (like bob, tbob, blast2html, ...). > >Updating blast 1.4 sources by replacing the 32 bits types by long integers >seem very hazardous ... > >Does someone here have the same problem, and some solution ? You don't specify what operating system you are using. I haven't looked at the BLAST 1.4 sources, but file offsets should always use the type off_t, rather than int. On IRIX at least, off_t is defined in . If you use this, your program will automatically be able to handle file size offsets as large as the OS can handle (for example in Solaris 2.x for x<6, off_t is 32 bits, which is why Solaris 2.5 and earlier had a maximum file size of 2 GB (approximately)). Similarly, malloc actually takes an argument of type size_t, not int. If you change the source to use that, you know that you will not end up giving malloc negative numbers, since (at least on IRIX), size_t is always an unsigned integer of some size (usually 32 or 64 bits, depending on your operating system). Tim. -- -------------------------------------------------------------------------- Dr T J R Cutts Tel: +44 1223 333596 Dept. of Biochemistry, 80 Tennis Court Rd. Cambridge, CB2 1GA, UK From owner-software@net.bio.net Mon Aug 03 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!island.idirect.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!newsfeed.nacamar.de!univ-lyon1.fr!pasteur.fr!nefertiti.pasteur.fr!letondal From: letondal@pasteur.fr (Catherine Letondal) Newsgroups: bionet.software Subject: blast 1.4 "too short" for the size of genbank and embl Date: 4 Aug 1998 09:22:05 GMT Organization: Institut Pasteur, Paris Lines: 27 Message-ID: <6q6jrt$h8p$1@desdemone.pasteur.fr> Reply-To: letondal@pasteur.fr (Catherine Letondal) NNTP-Posting-Host: nefertiti.pasteur.fr X-Trace: desdemone.pasteur.fr 902222525 17689 157.99.64.20 (4 Aug 1998 09:22:05 GMT) X-Complaints-To: usenet@pasteur.fr NNTP-Posting-Date: 4 Aug 1998 09:22:05 GMT X-Newsreader: mxrn 6.18-31 Hi, We maintain a copy of genbank (release + updates) as well as embl for blast 1.4 searches. The problem is that these databases have reached a size that exceeds a 32 bits integer capacity - and this version of blast is mainly based on such types of integer (more exactly 31 bits, for the integers are not unsigned). As a result, malloc of negative numbers occur. Of course, we also have the blast 2 NCBI and Washington-Univ. versions. We are aware that this version of blast is not maintained anymore at NCBI, but we keep the "old" 1.4 version of blast for compatibility reasons with blast output parsers (like bob, tbob, blast2html, ...). Updating blast 1.4 sources by replacing the 32 bits types by long integers seem very hazardous ... Does someone here have the same problem, and some solution ? Thanks in advance, -- Catherine LETONDAL letondal@pasteur.fr Tel: +33 (1) 40 61 31 91 Institut Pasteur Service d'Informatique Scientifique Fax: +33 (1) 40 61 30 80 28 rue du Docteur Roux 75724 Paris CEDEX 15 - FRANCE From owner-software@net.bio.net Mon Aug 03 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!oleane!pasteur.fr!nefertiti.pasteur.fr!letondal From: letondal@pasteur.fr (Catherine Letondal) Newsgroups: bionet.software Subject: Re: blast 1.4 "too short" for the size of genbank and embl Date: 4 Aug 1998 12:25:48 GMT Organization: Institut Pasteur, Paris Lines: 67 Message-ID: <6q6ukc$i1n$1@desdemone.pasteur.fr> References: <6q6jrt$h8p$1@desdemone.pasteur.fr> <6q6u66$j2v$1@pegasus.csx.cam.ac.uk> Reply-To: letondal@pasteur.fr (Catherine Letondal) NNTP-Posting-Host: nefertiti.pasteur.fr X-Trace: desdemone.pasteur.fr 902233548 18487 157.99.64.20 (4 Aug 1998 12:25:48 GMT) X-Complaints-To: usenet@pasteur.fr NNTP-Posting-Date: 4 Aug 1998 12:25:48 GMT X-Newsreader: mxrn 6.18-31 In article <6q6u66$j2v$1@pegasus.csx.cam.ac.uk>, tjrc1@mole.bio.cam.ac.uk (Tim Cutts) writes: >In article <6q6jrt$h8p$1@desdemone.pasteur.fr>, >Catherine Letondal wrote: >> >>Hi, >> >>We maintain a copy of genbank (release + updates) as well as embl for >>blast 1.4 searches. The problem is that these databases have reached a >>size that exceeds a 32 bits integer capacity - and this version of blast is >>mainly based on such types of integer (more exactly 31 bits, for the >>integers are not unsigned). As a result, malloc of negative >>numbers occur. >> >>Of course, we also have the blast 2 NCBI and Washington-Univ. versions. >>We are aware that this version of blast is not maintained anymore at NCBI, but >>we keep the "old" 1.4 version of blast for compatibility reasons >>with blast output parsers (like bob, tbob, blast2html, ...). >> >>Updating blast 1.4 sources by replacing the 32 bits types by long integers >>seem very hazardous ... >> >>Does someone here have the same problem, and some solution ? > >You don't specify what operating system you are using. I haven't >looked at the BLAST 1.4 sources, but file offsets should always use >the type off_t, rather than int. Sorry, I forgot. It's a DECalpha 4000 5/466 running Digital UNIX V4.0B. > >On IRIX at least, off_t is defined in . > >If you use this, your program will automatically be able to handle >file size offsets as large as the OS can handle (for example in >Solaris 2.x for x<6, off_t is 32 bits, which is why Solaris 2.5 and >earlier had a maximum file size of 2 GB (approximately)). > >Similarly, malloc actually takes an argument of type size_t, not int. > >If you change the source to use that, you know that you will not >end up giving malloc negative numbers, since (at least on IRIX), >size_t is always an unsigned integer of some size (usually 32 or 64 >bits, depending on your operating system). On Digital Unix: typedef unsigned long size_t; (We just are not sure about the consequences of changing blast 1.4 source code...) > >Tim. > > >-- >-------------------------------------------------------------------------- >Dr T J R Cutts Tel: +44 1223 333596 >Dept. of Biochemistry, 80 Tennis Court Rd. >Cambridge, CB2 1GA, UK > Catherine LETONDAL, Institut Pasteur Service d'Informatique Scientifique letondal@pasteur.fr 25 rue du Docteur Roux 75724 Paris CEDEX 15 - FRANCE tel: +33 (1) 40 61 31 91 fax: +33 (1) 40 61 30 80 From owner-software@net.bio.net Tue Aug 04 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!news.mel.connect.com.au!munnari.OZ.AU!news.unimelb.edu.au!ludwignt-4 From: murphy_r@licre.ludwig.edu.au (Roger Murphy) Newsgroups: bionet.software Subject: t-cell epitope prediction Date: Wed, 05 Aug 98 02:24:15 GMT Organization: Ludwig Institute for Cancer Research Lines: 22 Message-ID: <6q8j32$juo$1@izvestia.its.unimelb.edu.au> NNTP-Posting-Host: ludwignt-4.austin.unimelb.edu.au X-Newsreader: News Xpress 2.0 Beta #0 Does anyone know of any software that gives reasonable prediction of t-cell epitopes in proteins? This is for use on a WinNT platform, and I'm interested to find out about web-based, shareware or commerical software. Please reply to my email also. Thanks in advance. Roger Roger Murphy, Ph.D. Biological Production Facility Ludwig Institute for Cancer Research Austin & Repatriation Medical Centre Studley Road, Heidelberg, Vic. 3084 Australia. Tel 61-3-94965463 Fax 61-3-94965436 Email murphy_r@licre.ludwig.edu.au From owner-software@net.bio.net Tue Aug 04 23:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newsfeed.ecrc.net!newsfeed.nacamar.de!rill.news.pipex.net!pipex!server1.netnews.ja.net!leicester!pc5 From: ray@le.ac.uk (Raymond Dalgleish) Newsgroups: bionet.software Subject: Re: Turbo Pascal Date: Wed, 05 Aug 98 08:19:53 GMT Organization: Department of Genetics, University of Leicester, UK Lines: 7 Message-ID: <6q94j9$dtg_001@gene.le.ac.uk> References: <6q8bpr$s0u$1@news.tm.net.my> NNTP-Posting-Host: pc5.gene.le.ac.uk X-Newsreader: News Xpress Version 1.0 Beta #4 In article <6q8bpr$s0u$1@news.tm.net.my>, "ChanFong" wrote: >Where got download full version also latest version of turbo pascal??? >I really needed it > You go out and buy it! Raymond Dalgleish From owner-software@net.bio.net Tue Aug 04 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-peer.sprintlink.net!news.sprintlink.net!wn3feed!worldnet.att.net!204.127.161.34!worldnet!attbt2!mis2!worldnet!attbt1!mis1!news.abbott.com!news@abbott.com From: "Michael Anderson" Newsgroups: bionet.software Subject: Oligo v5.0 Date: 5 Aug 1998 23:05:54 GMT Organization: Abbott Laboratories Lines: 17 Message-ID: <01bdc0c5$e2255670$66b4f30a@andersom> NNTP-Posting-Host: 10.243.180.102 X-Newsreader: Microsoft Internet News 4.70.1162 Would anyone happen to be running Oligo v5.0 on Win95? I provide PC support for a large R&D firm and we have a user that is on Windows for Workgroups because nobody knows whether or not Oligo will work on a Win95 machine. My predecessors have taken the "if it ain't broke, don't fix it" attitude. I personally think that it is time to upgrade her machine to our current standards. I have looked for all references to this software on the internet and have come up empty. If you have any information that would be of help please forward it to me. Thanks Mike From owner-software@net.bio.net Tue Aug 04 23:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!newsfeed.internetmci.com!202.188.0.171!news.tm.net.my!not-for-mail From: "ChanFong" Newsgroups: bionet.software Subject: Turbo Pascal Date: Wed, 5 Aug 1998 09:13:04 +0800 Organization: TMnet Malaysia Lines: 4 Message-ID: <6q8bpr$s0u$1@news.tm.net.my> NNTP-Posting-Host: 202.188.183.178 X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Where got download full version also latest version of turbo pascal??? I really needed it From owner-software@net.bio.net Tue Aug 04 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: josephryan@yahoo.com Newsgroups: bionet.software Subject: Re: TWP-FreeWare Date: Wed, 05 Aug 1998 15:38:03 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 18 Message-ID: <6q9u8r$435$1@nnrp1.dejanews.com> References: <6q4uvm$jsg$1@news.vossnet.de> NNTP-Posting-Host: 165.112.191.175 To: comdes@vossnet.de X-Article-Creation-Date: Wed Aug 05 15:38:03 1998 GMT X-Http-User-Agent: Mozilla/4.05 [en] (X11; U; Linux 2.0.32 i586) FYI: You can translate German Web Pages to English using AltaVista... Try this... http://babelfish.altavista.digital.com/cgi-bin/translate?urltext=http://pages.vossnet.de/comdes/turbowin.htm In article <6q4uvm$jsg$1@news.vossnet.de>, "Häussler" wrote: > immernoch auf http://pages.vossnet.de/comdes/turbowin.htm > jedoch in neuem Layout und verbesserten Funktionen. > Gruss > F.Häussler > Sorry only in German > > -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-software@net.bio.net Tue Aug 04 23:00:00 1998 Path: biosci!CITYU.EDU.HK!BHRES From: BHRES@CITYU.EDU.HK (BHRES) Newsgroups: bionet.software Subject: Softwares look for inverted repeats Date: 5 Aug 1998 11:37:18 -0700 Organization: City University of Hong Kong Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Sir/Madam, Are there any web sites to help look for INVERTED REPEATS in a gene sequence? Many thanks. Richard Yu Email: 97420896@plink.cityu.edu.hk Department of Biology and Chemistry City University of Hong Kong Tat Chee Avenue, Kowloon Hong Kong From owner-software@net.bio.net Tue Aug 04 23:00:00 1998 X-newsreader: xrn 8.01 Newsgroups: bionet.info-theory,bionet.software Sender: fuellen@TechFak.Uni-Bielefeld.DE (Georg Fuellen) From: fuellen SPAMSTOP @techfak.uni-bielefeld.de (Georg Fuellen) Subject: Re: Bioinfomatics and PhD References: <35BA5852.FCA34F1E@ncl.ac.uk> Organization: Universitaet Bielefeld, Technische Fakultaet. To: Francisco.Pereira@ncl.ac.uk Cc: fuellen Reply-To: fuellen@techfak.uni-bielefeld.de NNTP-Posting-Host: schilf.techfak.uni-bielefeld.de Message-ID: <35c83cc3.0@news.uni-bielefeld.de> Date: 5 Aug 1998 13:06:43 +0200 X-Trace: 5 Aug 1998 13:06:43 +0200, schilf.techfak.uni-bielefeld.de Lines: 39 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.uni-bielefeld.de!techfak.uni-bielefeld.de!fuellen Xref: biosci bionet.info-theory:6485 bionet.software:21622 In article <35BA5852.FCA34F1E@ncl.ac.uk>, Francisco Pereira writes: |> Hello |> |> Could anybody tell me a good URL with links to Bioinformatics |> information ? |> I was also looking for good places to do a PhD in that area. Some EU programs in biocomputing/bioinformatics are listed at http://www.techfak.uni-bielefeld.de/bcd/ForAll/Econom/study.html (If you know a link that would fit there, just mail it and I'll fwd.) A collection of course syllabi is also available via http://www.techfak.uni-bielefeld.de/bcd/Curric/syllabi.html (Again, any comments, additions, corrections, etc would be welcome !) Here are some lists maintained elsewhere: http://www.iscb.org/training.html http://www.hgmp.mrc.ac.uk/GenomeWeb/docs-bioinf-course-info.html http://biotech.chem.indiana.edu/pages/bioinform/biprograms_us.html best wishes, Georg Fuellen Univ. Bielefeld, Research Group in Practical Comp. Science http://www.techfak.uni-bielefeld.de/bcd/welcome.html |> I have already browsed through the postings of this and other |> lists, but I would like more information ,if someone is able |> to give it. |> |> Thank you for your attention |> Francisco |> |> |> -- |> Francisco.Pereira@ncl.ac.uk .~. |> xico@oat.ncc.up.pt /V\ L I N U X |> xico@acm.org // \\ Do not fear the penguin |> /( )\ |> ^^-^^ From owner-software@net.bio.net Tue Aug 04 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!feed2.news.erols.com!erols!woodstock.news.demon.net!demon!news.demon.co.uk!demon!kovcomp.demon.co.uk!not-for-mail From: Warren Kovach Newsgroups: bionet.software Subject: ANN: MVSP 3.0 for Windows - pre-release version Date: Wed, 05 Aug 1998 10:25:00 +0100 Organization: Kovach Computing Services Message-ID: Reply-To: wlk@kovcomp.co.uk NNTP-Posting-Host: kovcomp.demon.co.uk X-NNTP-Posting-Host: kovcomp.demon.co.uk:158.152.48.110 X-Trace: news.demon.co.uk 902309095 nnrp-06:11228 NO-IDENT kovcomp.demon.co.uk:158.152.48.110 X-Complaints-To: abuse@demon.net Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Virtual Access by Ashmount Research Ltd, http://www.ashmount.com Lines: 25 Dear Colleagues, I have recently uploaded a pre-release version of MVSP 3.0 for Windows, the upcoming new version of our multivariate analysis package. This is a beta test version, released to give you an advanced look at it and to try it out on your system. Most of the features have been implemented and it has been extensively tested, so there should be just a few minor problems to iron out. Note that those who order MVSP 3.0 early (before 1 Oct. 1998) will receive a discount of approximately 25%. To find out more about the new features of MVSP 3.0 and to download a copy see the web page: http://www.kovcomp.co.uk/mvspbeta.html Warren Kovach -- Dr. Warren L. Kovach Internet: WarrenK@kovcomp.co.uk Kovach Computing Services tel./fax: +44-(0)1248-450414 85 Nant-y-Felin, Pentraeth, Anglesey Wales LL75 8UY U.K. WWW: http://www.kovcomp.co.uk/ From owner-software@net.bio.net Tue Aug 04 23:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!newsfeed.internetmci.com!195.99.66.215!news-feed1.eu.concert.net!news.ipcore.viaginterkom.de!newsfeed.vossnet.de!news.vossnet.de!not-for-mail From: "Häussler" Newsgroups: bionet.software Subject: TWP-FreeWare Date: Mon, 3 Aug 1998 20:20:17 +0200 Organization: Voss Net Communications GmbH Lines: 7 Message-ID: <6q4uvm$jsg$1@news.vossnet.de> NNTP-Posting-Host: s89.s.vossnet.de X-Trace: news.vossnet.de 902168374 20368 195.182.117.89 (3 Aug 1998 18:19:34 GMT) X-Complaints-To: abuse@vossnet.de NNTP-Posting-Date: 3 Aug 1998 18:19:34 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 immernoch auf http://pages.vossnet.de/comdes/turbowin.htm jedoch in neuem Layout und verbesserten Funktionen. Gruss F.Häussler Sorry only in German From owner-software@net.bio.net Wed Aug 05 23:00:00 1998 Newsgroups: bionet.software Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!vixen.cso.uiuc.edu!uchinews!harper.uchicago.edu!gluc From: Anton Gluck Subject: Re: announcement: Java mol. weight calculator In-Reply-To: <35B11610.94EA1C49@cs.uchicago.edu> X-Sender: gluc@harper.uchicago.edu X-Nntp-Posting-Host: harper.uchicago.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Message-ID: To: rna@net.bio.net Sender: news@midway.uchicago.edu (News Administrator) Reply-To: Anton Gluck Organization: University of Chicago -- Academic Computing Services Mime-Version: 1.0 Date: Thu, 6 Aug 1998 00:39:49 GMT Lines: 53 Hello again, As I have seen from the web server logs a fair number of people downloaded my program, which is really good. However, I have not received any feedback (with one exception - hi S.!), which is not so good. Were there any problems? Couldn't get it to work at all? Was it complete crap? Did it just leave you indifferent? I'm just trying to get a feeling of whether anybody is actually using the program, and what those people thought of it. I'd appreciate any feedback, Anton BTW: I have added mol. weight determination for proteins and have also redone the user interface to make it less confusing. I'll probably put this version on the web in the near future. If there is something that ought to be changed before I do that - let me know about it! For Mac users there's now also a StuffIt archive on the web page. On Sat, 18 Jul 1998, Anton Gluck wrote: > Hi there, > > I have been working on a molecular weight calculator, written in Java as > a stand alone application. I am working with a number of small RNA > oligomers, and had grown tired of manually calculating their molecular > weights. Because of this, my program right now works for RNA and DNA > only, but I am planning to add proteins to the next version. That is, if > there is a next version. That is why I am announcing my program here: > I'd like to know whether there is a general interest in such a program, > and therefore I'd really like to hear from you. Will you give my first > version a try and tell me what you think of it? I'm just testing the > waters here, and would appreciate any feedback. If no one other than > our lab is interested in such a program I won't be spending a whole lot > of time on it any more... > > You can find the program at > http://www-classes.cs.uchicago.edu/~gluc/MWC/MWC.html. The web page > contains some instructions on installing and running the program. The > program itself contains instructions also, although its use should be > pretty straightforward. The program is provided as a Java archive. > Macintosh users can download a double-click-able application in zip > compressed format as well. Naturally, the program will only run on > machines that have a Java Virtual Machine installed. > > Well, I hope to hear from you. Thanks for your attention, > > Anton > From owner-software@net.bio.net Wed Aug 05 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.wli.net!news2.ais.net!jamie!ais.net!news1.ispnews.com!news11.ispnews.com!not-for-mail From: "Andrew Miller" Newsgroups: bionet.software Subject: free medical image 3D visualization software for Windows95 Date: Thu, 6 Aug 1998 13:46:04 -0400 Organization: ISPNews http://ispnews.com Lines: 21 Message-ID: <6qcqb4$msd$1@news13.ispnews.com> NNTP-Posting-Host: computone19.infohouse.com Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Trace: news13.ispnews.com 902425764 23437 208.151.41.78 (6 Aug 1998 17:49:24 GMT) NNTP-Posting-Date: 6 Aug 1998 17:49:24 GMT X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Free medical image 3D visualization software for Windows95 brought to you by Cornell University/Division of Neurosurgery available at: http://users.infohouse.com/amiller/home.htm ... download size is 923 KB. The site also offers MRI & 3D test data. The application supports software rendering & hardware 3D accelerated graphics, as well as file support for DICOM, BMP, & RAW formats. NeuroModeller offers realtime 3D visualization and manipulation of surface iso-contours. Some of the features include: scrolling through multiple contours, superposition of contours, rotating, zooming, moving, lighting, texture mapping, coloring with transparency, and toggling on or off the visibility of contiguous regions. Image processing features of NeuroModeller include: window/level control, thresholding, pixel island removal, masking, and anisotropic diffusion. From owner-software@net.bio.net Wed Aug 05 23:00:00 1998 Path: biosci!lhc.nlm.nih.gov!not-for-mail From: walker@ncbi.nlm.nih.gov Newsgroups: bionet.software Subject: [ANNOUNCE] SEALS version 0.823 is available Date: 6 Aug 1998 21:20:45 GMT Organization: National Center for Biotechnology Information Lines: 17 Message-ID: <6qd6nd$knp$1@lhc.nlm.nih.gov> NNTP-Posting-Host: sky.nlm.nih.gov User-Agent: tin/pre-1.4-980618 (UNIX) (SunOS/5.6 (sun4u)) SEALS (A System for Easy Analysis of Lots of Sequences) version 0.823 is now available. This is a maintenance release, with yet more fixes and improvements to the install process, including several changes that allow SEALS to build and install correctly on Linux. For more information, see http://www.ncbi.nlm.nih.gov/Walker/SEALS One useful bit of functionality added in this release is that a complete manual, suitable for printing on a line printer, may be generated from the heretofore scattered documentation. Roland Walker From owner-software@net.bio.net Wed Aug 05 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!woodstock.news.demon.net!demon!news.demon.co.uk!demon!genesys.demon.co.uk!demon.co.uk!duncan From: "Dr. Duncan Clark" Newsgroups: bionet.software Subject: Re: Oligo v5.0 Date: Thu, 6 Aug 1998 10:08:09 +0100 Organization: GeneSys Ltd. Message-ID: <1XXVUBA5JXy1Ewrp@demon.co.uk> References: <01bdc0c5$e2255670$66b4f30a@andersom> Reply-To: "Dr. Duncan Clark" NNTP-Posting-Host: genesys.demon.co.uk X-NNTP-Posting-Host: genesys.demon.co.uk:158.152.17.110 X-Trace: news.demon.co.uk 902410958 nnrp-03:18366 NO-IDENT genesys.demon.co.uk:158.152.17.110 X-Complaints-To: abuse@demon.net MIME-Version: 1.0 X-Newsreader: Turnpike (32) Version 4.00 beta 9 Lines: 31 In article <01bdc0c5$e2255670$66b4f30a@andersom>, Michael Anderson writes >Would anyone happen to be running Oligo v5.0 on Win95? I provide PC >support for a large R&D firm and we have a user that is on Windows for >Workgroups because nobody knows whether or not Oligo will work on a Win95 >machine. My predecessors have taken the "if it ain't broke, don't fix it" >attitude. I personally think that it is time to upgrade her machine to our >current standards. > >I have looked for all references to this software on the internet and have >come up empty. > >If you have any information that would be of help please forward it to me. > Works fine on my machine running Win95. One minor problem is that I have my toolbar on the right hand side of the monitor rather than the bottom. Oligo5 does seem to know about this and on maximize doesn't take this into account. Slight niggle but easily workable around. Duncan -- The problem with being on the cutting edge is that you occasionally get sliced from time to time.... Duncan Clark DNAmp Ltd. Tel: +44(0)1252376288 FAX: +44(0)8701640382 http://www.dnamp.com http://www.genesys.demon.co.uk From owner-software@net.bio.net Wed Aug 05 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsxfer3.itd.umich.edu!news-peer.gip.net!news.gsl.net!gip.net!newsfeed.internetmci.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: mmahtani@iconixpharm.com Newsgroups: bionet.software Subject: SOFTWARE AND ALGORITHM DEVELOPMENT IN CHEMICAL-GENOMICS Date: Thu, 06 Aug 1998 14:24:19 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 52 Message-ID: <6qceai$iae$1@nnrp1.dejanews.com> NNTP-Posting-Host: 208.201.165.216 X-Article-Creation-Date: Thu Aug 06 14:24:19 1998 GMT X-Http-User-Agent: Mozilla/4.04 (Macintosh; U; PPC) Iconix Pharmaceuticals, Inc., a San Francisco Bay Area biopharmaceutical company, is seeking highly motivated individuals interested in pursuing an exciting career in the new area of Chemical Genomics. The company’s approach will advance the discovery process for human drugs through the systematic acquisition, integration and analysis of genetic and chemical information. State of the art information management and analysis tools are a key component of the approach. The successful candidate will join a growing team of computational scientists and software development experts. This team carries the responsibility to build and support the computational environment that is central to the success of the new enterprise. o DATABASE APPLICATION DEVELOPERS o o CHEMOINFORMATICS o BIOINFORMATICS o DATABASE APPLICATION DEVELOPERS are needed to design and build database applications and graphical user-interfaces to query and display biological, chemical and genetic data using Oracle and Web technologies. You will work in a team of scientists and engineers to develop applications that access information in a proprietary integrated drug discovery database. Candidates will have a Bachelor's degree in Computer Science, at least 5 years experience developing professional grade software, and experience building web-based Oracle applications and user-interfaces using Java, SQL, object-oriented design, JDBC and HTML. Formal training in biology or chemistry is a plus. COMPUTATIONAL SCIENTISTS are needed to develop and implement new algorithms for interpreting large, complex data sets generated from the interaction of many small molecules with numerous gene products. Ideal candidates will have a Ph.D. in computer science and demonstrated success in applying sophisticated computation to real-world problems (e.g. drug discovery, computational biology, object recognition, robotics, etc.). Experience in machine-learning, computational geometry, or physical modeling is beneficial, as is formal training in chemistry, biology, or physics. As the member of an interdisciplinary team, you will develop, implement, and apply novel algorithms to the interpretation of chemical and biological information. Candidates for these positions will have excellent communication skills, excellent work history and references, and the ability to work both independently and as part of a multidisciplinary team of scientists, including colleagues from biology, chemistry, genetics, and other fields. These are exciting opportunities for engineers and scientists with initiative, flexibility, and energy to contribute to a young organization that is emerging as a leader in its field. We offer competitive salaries, stock options and excellent benefits. Please send or fax your resume to: Human Resources Dept., Iconix Pharmaceuticals, Inc., 850 Maude Avenue, Mountain View, CA 94043. Attn: Computational Science Group #655-SJM. FAX (650) 526-3034, EMAIL hr@iconixpharm.com. Iconix Pharmaceuticals, Inc., is an Equal Opportunity Employer. -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-software@net.bio.net Thu Aug 06 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!lhc.nlm.nih.gov!not-for-mail From: Roland Walker Newsgroups: bionet.software Subject: [2nd try] [ANNOUNCE] SEALS version 0.823 is available Date: 7 Aug 1998 00:58:28 GMT Organization: National Center for Biotechnology Information Lines: 11 Message-ID: <6qdjfk$hho$1@lhc.nlm.nih.gov> NNTP-Posting-Host: sky.nlm.nih.gov User-Agent: tin/pre-1.4-980618 (UNIX) (SunOS/5.6 (sun4u)) There was one script which escaped the SEALS update that was just posted, and there were some superfluous object files left in one of the module directories. The archive is now corrected as of 8.45 pm EST; if you have already downloaded it, you should fetch the new one. Sorry for any inconvenience. Roland From owner-software@net.bio.net Thu Aug 06 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.internetmci.com!158.43.192.17!rill.news.pipex.net!pipex!sun4nl!212.206.254.2.MISMATCH!newnews.nl.uu.net!not-for-mail From: "Jan Hoolwerf" Newsgroups: bionet.software Subject: Oligo v5.0 Date: Fri, 07 Aug 1998 10:31:05 +0100 Organization: The Fractal Lover Lines: 21 Message-ID: <00001120@elcom.org> References: <1XXVUBA5JXy1Ewrp@demon.co.uk> NNTP-Posting-Host: ah51-51.arnhem.nl.net X-Gateway: NewsGate v1.0 gamma 2 NNTP <-> FidoNet Gateway X-FTNADDR: 2:283/211.0 Hello, DDC> One minor problem is that I have my toolbar on the right hand side DDC> of the monitor rather than the bottom. Oligo5 does seem to know DDC> about this and on maximize doesn't take this into account. Slight DDC> niggle but easily workable around. More programs show this behaviour and there's a little program that solves this problem. It's called SHOVE-IT and the url i have is http://members.aol.com/phord although i'm not sure if that is still valid. But it should be easily found via e.g. AltaVista. regards, Jan Hoolwerf + email : hoolwerf@solair.inter.nl.net + FidoNet: 2:283/211 + http://www.geocities.com/SiliconValley/Heights/6174/ From owner-software@net.bio.net Thu Aug 06 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!logbridge.uoregon.edu!priori!news.he.net!sws1.ctd.ornl.gov!PSTCC7.pstcc.cc.tn.us!news.memphis.edu!news.wku.edu!not-for-mail From: Mike Stokes Newsgroups: bionet.software Subject: job--biology instructor/multimedia devoloper Date: Mon, 03 Aug 1998 14:18:34 -0500 Organization: Western Kentucky University Lines: 80 Message-ID: <35C60D0A.BBD8EA20@wku.edu> Reply-To: Michael.Stokes@wku.edu NNTP-Posting-Host: stokesmk.tcnw.wku.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.wku.edu 902171893 18112 161.6.6.49 (3 Aug 1998 19:18:13 GMT) X-Complaints-To: postmaster@wku.edu NNTP-Posting-Date: 3 Aug 1998 19:18:13 GMT X-Mailer: Mozilla 4.05 [en] (Win95; U) Biology Instructor/ Multimedia Specialist 12-month, renewable, non-tenure track position in Biology. Duties will be divided between teaching introductory biology and helping other faculty develop multimedia content for both site- and distance-based teaching, especially via the Internet. The candidate must have a Ph.D. in some area of the biological sciences and demonstrated proficiency with multimedia development including the emerging Internet technologies (e.g. HTML, Java, Shockwave/Flash, Streaming Audio/Video, etc.). Demonstrated proficiency in teaching biology at the introductory level is required. The candidate will be expected to use the introductory biology courses to showcase these technologies and to provide the non-majors course over the Internet within the framework of an emerging state-wide virtual university system. The successful candidate will develop innovative and engaging materials relevant to introductory non-majors biology students. The candidate must be able to work in a collaborative environment and be capable of directing student work. Committee and university service duties will be minimal. The Biology Department has complete multimedia development facilities, including Macintosh- and Windows-based multimedia platforms, an SGI O2 Studio bundle, a departmental IP server, and complete campus-wide networking. Starting salary is $36,000 per annum. Please send the following materials to Chair, Media Specialist Search, Department of Biology, Western Kentucky University, Bowling Green, KY 42101. Western Kentucky University is an equal opportunity employer. Resume A portfolio of multimedia instructional materials that you have developed. Include WWW-based content or URLs for appropriate sites. A statement of teaching strategy, including an outline for an innovative and relevant introductory non-majors course, and evidence of your teaching effectiveness. Three letters of recommendation from persons who have knowledge of your teaching and multimedia development abilities. Applications will be reviewed beginning August 15 based on the following criteria: Basic qualifications: a. Ph.D. in biological science b. Demonstrated proficiency in multimedia development as evidenced by portfolio c. Demonstrated teaching proficiency and innovation d. Ability to work collaboratively in developing multimedia material Desirable qualifications: a. Ability to develop interactive web-based multimedia b. Proficient in HTML c. Proficient in Java d. Able to do animation (Director/Flash) e. Knowledge of video editing/development f. Ability to direct students in multimedia and web development -- Michael Stokes Department of Biology Western Kentucky University Bowling Green, Ky 42101 Michael.Stokes@wku.edu http://bioweb.wku.edu/stokes/ -- Michael Stokes Department of Biology Western Kentucky University Bowling Green, Ky 42101 Michael.Stokes@wku.edu http://bioweb.wku.edu/stokes/ From owner-software@net.bio.net Fri Aug 07 23:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!newshub.northeast.verio.net!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!cam-news-feed1.bbnplanet.com!news.bbnplanet.com!news.delphi.com!news From: rbcaldwell@delphi.com Newsgroups: bionet.software Subject: Final CFP -- JCIF special issue (data mining and financial news) Date: Sat, 8 Aug 98 13:17:44 -0500 Organization: Delphi (info@delphi.com email, 800-695-4005 voice) Lines: 212 Message-ID: NNTP-Posting-Host: 199.93.4.2 ******************************************************************* F I N A L C A L L F O R P A P E R S ******************************************************************* Journal of Computational Intelligence in Finance Final Call for Papers Special Issue on "Financial News Analysis using Distributed Data Mining" The Journal of Computational Intelligence in Finance, a peer-reviewed technical journal, published by Finance & Technology Publishing, is seeking papers for review and publication on "Financial News Analysis using Distributed Data Mining". The Journal of Computational Intelligence in Finance publishes applied research and practical applications of high quality that are based on sound theoretical, empirical or quantitative analysis. For practitioners and applied researchers, JCIF serves as the journal of record on "the application of advanced computational technologies and analytical techniques for financial modeling, investing and trading, and risk management." Papers published in JCIF are eligible for the "Distinguished Essay on Computational Intelligence in Finance" award, which is selected by the Editorial Board each year. EDITORIAL BOARD Randall B. Caldwell, Editor-in-Chief Emilio Barucci - University of Florence, Italy Richard J. Bauer, Jr. - St. Mary's University, Texas Neil Burgess - London Business School Oscar Castillo - UABC University, California Jerry Connor - London Business School Eric de Bodt - Universite Catholique de Louvain, France James F. Derry - Mgmt. Engineering Productivity Systems, Ohio Athanasios Episcopos - National Bank of Greece Andrew Flitman - Monash University, Australia Susan Garavaglia - Dun and Bradstreet, New Jersey Ramo Gencay - University of Windsor, Canada Sabyasachi Ghoshray - Florida International University Lee Giles - NEC Research Institute, New Jersey Christian Haefke - University of California at San Diego Ypke Hiemstra - Vrije Universiteit, The Netherlands Jason Kingdon - Searchspace Limited, University College London Ralph Neuneier - Siemens AG Corporate Research Center, Germany Zoran Obradovic - Washington State University Marimuthu Palaniswami - University of Melbourne Carlos E. Pedreira - Catholic University, Rio Stuart H. Rubin - Central Michigan University David B. Skalak - IBM, New York Leon Sterling - University of Melbourne Manoel F. Tenorio - Purdue University, Indiana Halbert White - University of California at San Diego Lei Xu - The Chinese University of Hong Kong SPECIAL TOPIC Financial News Analysis using Distributed Data Mining PAPERS DUE September 15, 1998 ACCEPTANCE NOTIFICATION November 30, 1998 FINAL REVISED MANUSCRIPTS DUE January 15, 1999 PUBLICATION DATE March 1999 GUEST EDITORS Zoran Obradovic Stuart H. Rubin Associate Professor Associate Professor Elec. Eng. & Comp. Sci. Dept. of Comp. Sci. Washington State University Central Michigan University Pullman, WA 99164-2752, USA Mt. Pleasant, MI 48859, USA zoran@eecs.wsu.edu rubin@cps.cmich.edu FOR THE LATEST AND MOST COMPLETE INFORMATION ON THIS CALL, SEE: http://ourworld.compuserve.com/homepages/ftpub/call.htm MOTIVATION Recent technological developments, the rapid growth of the World Wide Web, and maturing corporate intranet structures have led to the rapid dissemination of huge amounts of financial news and information (newspaper articles, financial services information, corporate publications, stock exchange news, peer-reviewed financial journal articles, etc.). However, cost and time constraints prohibit an exhaustive search through or download of all potentially relevant financial news and information available on the Internet, for later analysis and processing. One possible solution is to distribute information sampling over a large number of locations in order to classify local data, construct a pool of relevant information, and generate useful rules that might be further analyzed or processed at a central location. This requires intelligent and dynamic domain decomposition, as well as flexible software agents for symbolic information processing. SCOPE All papers submitted must focus on the data mining of financial news and information, and on applications of interest to financial analysis or decision-making, investing or trading. Of particular interest are algorithms and techniques that both incorporate computational intelligence and are unique or especially relevant to financial tasks. Authors are invited to submit papers on the design of automated, scalable, distributed knowledge discovery systems for financial information mining on the Internet, to address issues related to: - search strategies - knowledge representation - reasoning mechanisms - learning algorithms Suggested topics include but are not limited to the following: - intelligent software agent structures - sampling strategies for mining the World Wide Web - distributed search algorithms for mining financial news - collaborative and heuristic search methods - statistical text mining - incremental knowledge discovery methods - financial news and information quality - dynamic domain decomposition - expert and decision-based strategies - knowledge representation issues - knowledge-base design and segmentation - communications and query issues - Knowledge Interchange Format (KIF) - Knowledge Query and Manipulation Language (KQML) - semantic nets and frames - combining natural language processing and statistical text mining - algorithms for organizing, filtering and summarizing textual information - state space methods and issues - novel learning and reasoning algorithms ABSTRACTS Submit 150 to 300 word abstract including full name(s) and affiliation(s) of the author(s), complete mailing address and telephone numbers of all authors. Authors should provide a brief biographic sketch of themselves. Send abstracts to: Post: JCIF, P.O. Box 764, Haymarket, VA 20168 USA E-mail: ftpub@compuserve.com Fax: 1-703-753-2634 PAPERS Papers must not have been previously published or currently submitted for publication elsewhere. All material must be provided in the English language. Submit three copies of each paper. Papers must be formatted for 8.5x11-inch page format. Authors should provide a brief biographic sketch of themselves. Each copy submitted should include a page that contains the title of the paper, the full name(s) and affiliation(s) of the author(s), complete mailing address and telephone numbers of all authors, and a 150 to 300 word abstract. The Journal reserves the right to edit all material to meet space requirements and to make grammatical and typographical corrections. The final text should be 4000 to 6000 words in length, contain no more than 15 references, and be provided as follows: (1) Hardcopy: printed and double-spaced, with notations for the location of graphics, mathematical equations, given thereon, as necessary, (2) Softcopy: The REQUIRED MEDIA FORMAT is IBM PC 3.5", 1.44MB. The PREFERRED FILE FORMAT is Word for Windows 3.1/95 (Word 6/7/97). Other acceptable software file formats are the following: Tex and LaTex using the required media format (Scientific Workplace 3.0 preferred, use standard features) The PREFERRED GRAPHICS formats are Windows 3.1/95 (*.bmp,*.wmf,*.eps). For other graphics formats, submit high-quality, camera-ready hardcopy, or make an inquiry. Include pseudo-code or source code in separate figures (listings). Extensive code listings may be published on the Web site because of space limitations in the journal. Text citations must use the following format: last name(s) of author(s), publication date and suffix (as necessary) in brackets. Example: (a) direct reference: Watkins and McCoy [1993a] (b) indirect reference: [Watkins and McCoy 1993a] References must be listed alphabetically by the last name of the first author according to the following formats: Journal Article: authors' names, publication date and suffix (as necessary) in brackets, article title (in double quotations), periodical title (in italics), volume and number, pages cited. Book: authors' names, publication date and suffix (as necessary) in brackets, book title (in italics), publisher, publisher location, pages cited. Chapter in Book/Proceedings: authors' names, publication date and suffix (as necessary) in brackets, chapter title (in double quotations), editors' names, book title (in italics), publisher, location, pages cited. Send all manuscripts by Post to: Editors, JCIF, P.O. Box 764, Haymarket, VA 20168 USA ******************************************************************* F I N A L C A L L F O R P A P E R S ******************************************************************* From owner-software@net.bio.net Fri Aug 07 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!ptdnetP!newsgate.ptd.net!news.cc.ukans.edu!not-for-mail From: PGegen@UKans.edu (Dr. Peter Gegenheimer) Newsgroups: bionet.software Subject: Re: Turbo Pascal Date: 8 Aug 1998 00:03:12 GMT Organization: Univ. Kansas (Biochemistry) Lines: 31 Message-ID: <7opiGDf98QgB-pn2-dd0L42PT9R8v@rnaworld.bio.ukans.edu> References: <6q8bpr$s0u$1@news.tm.net.my> <6q94j9$dtg_001@gene.le.ac.uk> Reply-To: PGegen@UKans.edu NNTP-Posting-Host: rnaworld.bio.ukans.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-Newsreader: ProNews/2 Version 1.00 On Wed, 5 Aug 1998 08:19:53, ray@le.ac.uk (Raymond Dalgleish) wrote: > In article <6q8bpr$s0u$1@news.tm.net.my>, "ChanFong" wrote: > >Where got download full version also latest version of turbo pascal??? > >I really needed it > > > You go out and buy it! > > Raymond Dalgleish Ray, you made my day! Sort & sweet - I've said the same thing many times but it takes me a paragraph. o------------------------------------------------------------------- --o | Dr. Peter Gegenheimer | Vox: 785-864-3939 FAX: 785-864-5321 | | Departments of Biochemistry | PGegen@UKans.edu | | and of Botany | http://RNAworld.Bio.UKans.edu/ | | | | | University of Kansas | | | 2045 Haworth Hall | "The sleep of reason produces | | Lawrence KS 66045-2106 | monsters." Goya | o_____________________________|_____________________________________ __o From owner-software@net.bio.net Sat Aug 08 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news.sprintlink.net!130.207.244.18!gatech!news-relay.ncren.net!ussun2n!news@ussun2n.glaxo.com From: United Earth Alliance Newsgroups: bionet.software Subject: Help.... Date: Sun, 09 Aug 1998 16:30:57 +0100 Organization: UEA Lines: 15 Message-ID: <35CDC0B1.55FDFC43@rocketmail.com> NNTP-Posting-Host: 147.184.168.172 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (WinNT; I) How about using your unique skills to help those that need your help? We all have skills that others lack, and we lack skills, others have. The UEA seeks to bring together people who are willing to work together, sharing their strengths and weaknesses. If you are interested in finding out more please visit our website at http://www.uea.net Thank you for your time UEA -- United Earth Alliance Small Step. Right Direction. http://www.uea.net From owner-software@net.bio.net Sat Aug 08 23:00:00 1998 Newsgroups: comp.sys.mac.scitech,alt.med.software,bionet.software Subject: [ANNOUNCE] Bookends Plus from Sonny Software Organization: nih X-Posted-From: InterNews 1.1@pm9-181.his.com Lines: 52 Xdisclaimer: No attempt was made to authenticate the sender's name. From: jda@his.com (jda) Sender: -Not-Authenticated-[4091] NNTP-Posting-Host: pm9-181.his.com Message-ID: <35cd8bcb.0@news4.his.com> Date: 9 Aug 98 11:45:15 GMT Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!207.97.14.174!europa.clark.net!207.106.0.20!news-xfer.netaxs.com!news4.his.com!pm9-181.his.com BETHESDA, MD--July 16, 1998--Sonny Software releases a new version of Bookends Plus, the most complete reference and information management application for the Macintosh. Sonny Software is pleased to announce that it has acquired the rights to Bookends Plus, a leading reference management/bibliography generation application created exclusively for the Macintosh, from Westing Software. As a Mac-first and Mac-only product, Bookends has long been a leader in adopting MacOS technologies, including AppleEvents, QuickTime, and Apple Guide on-line help. Bookends is also the only Macintosh product of its kind that can serve its contents on the Web in real-time, allowing multiple users to share, and even add or edit, information with users around the world on any platform. Sonny Software will mark its acquisition of Bookends Plus with the launch of a new version, 4.1, and a reduction in price. Among the improvements are: ¥ Bookmark web sites in Bookends and go to them directly from a Bookends database. ¥ Import references directly from the clipboard (makes importing references from the web a snap). ¥ The ability to format a footnote differently depending on whether it is being cited for the first time or after an initial citation. This is particularly useful for footnotes or bibliographies using styles for the humanities. ¥ Expanded graphics support. You can view any type of document supported by QuickTime 3 (available at no cost from Apple Computer). In conjunction with the Attach feature, this means that you can examine virtually any kind of graphic (diagram, picture, plasmid map, chemical structure, even video) from within Bookends. ¥ Web users can edit references in a Bookends database via the web (with a password protection option). With the release of version 4.1, Sonny Software is also pleased to announce a reduction in price for Bookends Plus: $99 for first-time buyers. It is available to students for $69 (proof of enrollment required). Upgrades for users of Bookends Plus 4.x are $39 and for users of Bookends Pro/Bookends Web 3.x are $49. A free evaluation copy of Bookends Plus can be downloaded from the Sonny Software web site (www.sonnysoftware.com). All features are enabled in the evaluation copy except that databases are limited to a maximum of 15 references. Once purchased, Sonny Software will supply a registration number that will "unlock" the evaluation version and remove this restriction. Visit our web site to learn more about Bookends and download an evaluation copy and complete electronic manual. Sonny Software 8903 Seneca Lane Bethesda, MD 20817 www.sonnysoftware.com Contact: jda@sonnysoftware.com From owner-software@net.bio.net Sat Aug 08 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!newsfeed.internetmci.com!195.99.66.215!news-feed1.eu.concert.net!news.ipcore.viaginterkom.de!newsfeed.vossnet.de!news.vossnet.de!not-for-mail From: "Häussler" Newsgroups: bionet.software Subject: Re: TWP-FreeWare Date: Sun, 9 Aug 1998 16:23:09 +0200 Organization: Voss Net Communications GmbH Lines: 19 Message-ID: <6qkb9e$opt$2@news.vossnet.de> References: <6q4uvm$jsg$1@news.vossnet.de> NNTP-Posting-Host: s97.s.vossnet.de X-Trace: news.vossnet.de 902672494 25405 195.182.117.97 (9 Aug 1998 14:21:34 GMT) X-Complaints-To: abuse@vossnet.de NNTP-Posting-Date: 9 Aug 1998 14:21:34 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Un dazu noch. Probleme mit immer zuvielen *.TMP *.BAK etc. Dateien? Gut dann holt euch DELALLE. Löscht (einstellbar) bestimmtbare Dateitypen auf beliebig einstellbaren Laufwerken. FreeWare ca.80KB F.Häussler http://pages.vossnet.de/comdes/turbowin.htm Häussler schrieb in Nachricht <6q4uvm$jsg$1@news.vossnet.de>... >immernoch auf http://pages.vossnet.de/comdes/turbowin.htm >jedoch in neuem Layout und verbesserten Funktionen. >Gruss >F.Häussler >Sorry only in German > > From owner-software@net.bio.net Sat Aug 08 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.direct.ca!mr.net!news.mr.net!not-for-mail From: "KingSky" Newsgroups: alt.comp.software.tools,bionet.software,biz.comp.software,biz.comp.software.demos,comp.os.ms-windows.apps.compatibility.win95 Subject: A lot of FREEWARE! Date: Sun, 9 Aug 1998 02:03:03 -0400 Organization: [poster's organization not specified] Lines: 12 Message-ID: <6qkuav$p7n$2@news3.mr.net> NNTP-Posting-Host: aa130.ips.paulbunyan.net X-Newsreader: Microsoft Outlook Express 4.72.3115.0 X-Mimeole: Produced By Microsoft MimeOLE V4.72.3110.3 Come and check out my fresh, constantly updated freeware page at Http://freeloader.simplenet.com/index.html! It has loads of software for Windows 95/98 and NT. All the newest browsers, multimedia, plug-ins, business programs, graphics and internet utilities. Visit often, and Load Up On FreeWare! Thanks for Reading! WebMaster http://freeloader.simplenet.com/index.html Load up on FreeWare!! From owner-software@net.bio.net Sun Aug 09 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!newshub.northeast.verio.net!news-feeder.onramp.net!news.onramp.net!not-for-mail From: Wayne Parrott Newsgroups: bionet.software Subject: help: blast win32 setup Date: Mon, 10 Aug 1998 02:22:47 -0500 Organization: WorkingObjects.com Lines: 35 Message-ID: <35CE9FC7.67EA682A@workingobjects.com> NNTP-Posting-Host: ppp16-24.dllstx.onramp.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (WinNT; I) Problem: formatting blast db with formatdb.exe Situation: 1) downloaded and unzipped the Blast win32 executables into dir e:\blast 2) created ncbi.ini with contents [NCBI] Data=e:\blast\data 3) downloaded the ecoli.aa database from ftp://ncbi.nlm.nih.gov/blast/db/ into dir e:\blast 4) ran formatdb as follows >cd e:\blast >formatdb -i ecoli.aa 5) formatdb.log has contents ========================[ Aug 10, 1998 1:16 AM ]======================== Version 2.0.5 [May-5-1998] Started database file "ecoli.aa" FATAL ERROR: [067:001] FindPath failed FATAL ERROR: [067:000] Failure to read sequence. FastaToSeqEntry() failed. Formated 0 sequences 6) set env NCBI=e:\tmp\blast I am assuming formatdb is unable to locate the db file "ecoli.aa". Any clues as to what I'm doing incorrectly? --------------------------------------------------------------------- Wayne Parrott email: wayne@workingobjects.com | WorkingObjects.com voice: (972)491-3704 | web: http://www.workingobjects.com | --------------------------------------------------------------------- "The main thing, is to keep the main thing, the main thing" lyrics by Scott Krippayne From owner-software@net.bio.net Sun Aug 09 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newshub.northeast.verio.net!nntp.newengland.verio.net!news.pn.com!news-feeder.onramp.net!news.onramp.net!not-for-mail From: Wayne Parrott Newsgroups: bionet.software Subject: Re: help: blast win32 setup Date: Mon, 10 Aug 1998 13:44:35 -0500 Organization: WorkingObjects.com Lines: 43 Sender: parrott@p47.amax26.dialup.dal1.flash.net Message-ID: <35CF3F93.949B58CB@workingobjects.com> References: <35CE9FC7.67EA682A@workingobjects.com> NNTP-Posting-Host: p47.amax26.dialup.dal1.flash.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (WinNT; I) Problem resolved. Thanks to Scott McGinnis at NLM for pointing out that I forgot to locate the ncbi.ini config file in a system directory (dah!). Thanks Scott. W Wayne Parrott wrote: > > Problem: formatting blast db with formatdb.exe > > Situation: > 1) downloaded and unzipped the Blast win32 executables into dir e:\blast > 2) created ncbi.ini with contents > [NCBI] > Data=e:\blast\data > 3) downloaded the ecoli.aa database from > ftp://ncbi.nlm.nih.gov/blast/db/ into dir e:\blast > 4) ran formatdb as follows > >cd e:\blast > >formatdb -i ecoli.aa > 5) formatdb.log has contents > ========================[ Aug 10, 1998 1:16 AM > ]======================== > Version 2.0.5 [May-5-1998] > Started database file "ecoli.aa" > FATAL ERROR: [067:001] FindPath failed > FATAL ERROR: [067:000] Failure to read sequence. FastaToSeqEntry() > failed. > > Formated 0 sequences > 6) set env NCBI=e:\tmp\blast > > I am assuming formatdb is unable to locate the db file "ecoli.aa". Any > clues as to what I'm doing incorrectly? > > --------------------------------------------------------------------- > Wayne Parrott email: wayne@workingobjects.com | > WorkingObjects.com voice: (972)491-3704 > | > web: http://www.workingobjects.com | > --------------------------------------------------------------------- > "The main thing, is to keep the main thing, the main thing" > lyrics by Scott Krippayne From owner-software@net.bio.net Sun Aug 09 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!wn3feed!worldnet.att.net!135.173.83.225!attworldnet!newsadm From: "Willy Valdivia" Newsgroups: bionet.software Subject: Mutation Sofware Date: 10 Aug 1998 00:35:12 GMT Organization: AT&T WorldNet Services Lines: 51 Message-ID: <6qlf80$8n1@bgtnsc02.worldnet.att.net> NNTP-Posting-Host: 12.68.96.241 Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00A0_01BDC3D5.8FCBF240" X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 This is a multi-part message in MIME format. ------=_NextPart_000_00A0_01BDC3D5.8FCBF240 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear subscribers: I am interested in study mutations produced by ionizing radiation in = plant cell models. Someone know about software that can help me to = estimate the mutation frequencies or DNA damage or strand breaks. Which = is the most used codes or simulations in animal systems. Thank you. Willy Valdivia=20 ------=_NextPart_000_00A0_01BDC3D5.8FCBF240 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear = subscribers:
 
I am interested in = study mutations=20 produced by ionizing radiation in plant cell models. Someone know about = software=20 that can help me to estimate the mutation frequencies or DNA damage or = strand=20 breaks. Which is the most used codes or simulations in animal=20 systems.
 
Thank you.
 
Willy=20 Valdivia 
------=_NextPart_000_00A0_01BDC3D5.8FCBF240-- From owner-software@net.bio.net Mon Aug 10 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!la-news-feed1.bbnplanet.com!news.bbnplanet.com!newsfeed1.earthlink.net!cyclone.news.idirect.com!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: G.Vidarsson@Pobox.accu.uu.nl Newsgroups: bionet.software Subject: ELISA program TITRI - Distribution file fixed Date: Tue, 11 Aug 1998 07:52:22 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 35 Message-ID: <6qot7l$c25$1@nnrp1.dejanews.com> NNTP-Posting-Host: 131.211.169.75 X-Article-Creation-Date: Tue Aug 11 07:52:22 1998 GMT X-Http-User-Agent: Mozilla/4.05 [en] (Win95; I) The 32 bit version (for Windows 95 and greater) of the ELISA program Titri, version 5.01, is now available for download at http://members.tripod.com/~gestur/programs/titri.htm * To install - run the distribution EXE file (Titri.exe or Titri32.exe) to unzip necessary files to a temporary folder. Then run "Setup.EXE" * This software is totally free for all possible uses. * Version 5.01 is virtually the same as 4.74, but compiled using Visual Basic 5.0 instead of VB 4.0 (respectively). This might result in some bugs, but also, according to Microsoft, in faster code. * Source code is available upon request All the best, Gestur Vidarsson, Department of Immunology, University Hospital Utrecht (AZU) Rm G04.614 Heidelberglaan 100 3584 CX Utrecht The Netherlands TEL +31 (0)30 253 3925 / 250 6520 FAX +31 (0)30 250 5449 -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-software@net.bio.net Mon Aug 10 23:00:00 1998 Path: biosci!NCBI.NLM.NIH.GOV!francis From: francis@NCBI.NLM.NIH.GOV Newsgroups: bionet.software Subject: Re: Translation of protein sequence to nucleotide sequence Date: 11 Aug 1998 04:28:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 75 Sender: daemon@net.bio.net Distribution: world Message-ID: <199808111125.HAA12978@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net sorry Tony, you are right, I totally missed your point .. (as Tim Littlejohn also pointed out to me) ...Your posting was not ambiguious, it was I who missread it ... sorry, I have no suggestions, but others may have ... regards, f. -- | B.F. Francis Ouellette | GenBank Coordinator | | francis@ncbi.nlm.nih.gov > From mcbaet@mcbsgs1.imcb.nus.edu.sg Tue Aug 11 01:08:09 1998 > X-Sender: mcbaet@imcb.nus.edu.sg > Date: Tue, 11 Aug 1998 13:08:53 +0800 > To: francis@ncbi.nlm.nih.gov > From: Anthony Ting > Subject: Re: Translation of protein sequence to nucleotide sequence > > Dear Francis, > > Thanks for the prompt reply. While ORF Finder is a nice program. It does > the opposite of what I want. I already have a protein sequence, what I > want to do is convert to nucleotide sequence given a specific codon usage > table. I'm sorry if my original posting was ambiguious. If you have any > suggestions, I'd really appreciate it. Otherwise, I'm spending the next > few days doing it manually. > > thanks again, > > Tony > > > > At 11:53 PM 8/10/98 -0400, you wrote: > > > >> From: mcbaet@MCBSGS1.IMCB.NUS.EDU.SG (Anthony Ting) > > > >=-> Is anyone aware of a program that translate a protein > >=-> sequence into > >=-> a nucleotide sequence given a specific codon usage table? > > > >Dear Anthony Ting, > > > >have a look ORF Finder at: > > > >http://www.ncbi.nlm.nih.gov/gorf/gorf.html > > > >I think it will do what you want (and a little bit more :-) > > > >cheers, > > > >francis > > > >-- > >| B.F. Francis Ouellette > >| GenBank Coordinator > >| > >| francis@ncbi.nlm.nih.gov > > > > > > > > > > > > ------------------------------------------------------------------- > Anthony Ting, PhD phone: 65-874-7846 > Institute of Molecular and Cell Biology fax: 65-779-1117 > 30 Medical Drive > Singapore 117609 > From owner-software@net.bio.net Mon Aug 10 23:00:00 1998 Path: biosci!MCBSGS1.IMCB.NUS.EDU.SG!mcbaet From: mcbaet@MCBSGS1.IMCB.NUS.EDU.SG (Anthony Ting) Newsgroups: bionet.software Subject: Translation of protein sequence to nucleotide sequence Date: 10 Aug 1998 20:17:55 -0700 Organization: Institute of Molecular & Cell Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <35CEA9D3.AE38C855@imcb.nus.edu.sg> NNTP-Posting-Host: net.bio.net Hi there, Is anyone aware of a program that translate a protein sequence into a nucleotide sequence given a specific codon usage table? thanks, Anthony Ting From owner-software@net.bio.net Mon Aug 10 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!newsfeed.internetmci.com!204.210.0.20!news.san.rr.com!not-for-mail From: risaacson@physics.ucsd.edu (Roger Isaacson) Newsgroups: bionet.software Subject: Re: Endnote writer for the PC Organization: UCSD Physics Message-ID: <35d0b3d2.498174@news-server> References: <35B9FBEB.20A6@magnus.acs.ohio-state.edu> <6qo3ob$7o3$1@nnrp1.dejanews.com> X-Newsreader: Forte Agent 1.5/32.451 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 34 Date: Tue, 11 Aug 1998 03:04:14 GMT NNTP-Posting-Host: 204.210.41.117 NNTP-Posting-Date: Mon, 10 Aug 1998 20:04:14 PDT On Tue, 11 Aug 1998 00:37:31 GMT, sales@biblioscape.com wrote: ->Hi Arffaan, -> ->If you use Windows 95, 98, or NT4, you can try a bibliographic software called ->Biblioscape. You can download a fully functional trial copy at ->www.biblioscape.com -> ->Paul -> ->In article <35B9FBEB.20A6@magnus.acs.ohio-state.edu>, -> arfaan Rampersaud wrote: ->> When I had my macintosh there was a program that allowed me to save ->> references from the Reference Update software program to the Endnotes ->> bibliographic software. I believe the program was called Endnote ->> Writer. I am now using a PC and would like to find out if something ->> similar is available for Windows. ->> ->> Thanks ->> ->> Arfaan Rampersaud ->> I use EndNote Plus from http://www.niles.com/ Roger Isaacson risaacson@physics.ucsd.edu UCSD Physics Dept PH 619-534-2505 9500 GILMAN DRIVE FAX 619-822-0007 LA JOLLA CA 92093-0319 From owner-software@net.bio.net Mon Aug 10 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!newsfeed.internetmci.com!204.210.0.20!news.san.rr.com!not-for-mail From: risaacson@physics.ucsd.edu (Roger Isaacson) Newsgroups: bionet.software Subject: Re: xwindows clinet Organization: UCSD Physics Message-ID: <35cfb338.343877@news-server> References: <35C4A854.F282DE16@accefyn.org.co> X-Newsreader: Forte Agent 1.5/32.451 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 18 Date: Tue, 11 Aug 1998 02:59:55 GMT NNTP-Posting-Host: 204.210.41.117 NNTP-Posting-Date: Mon, 10 Aug 1998 19:59:55 PDT On 2 Aug 1998 10:58:18 -0700, acad@ACCEFYN.ORG.CO (Alexander Garcia) wrote: ->Where can I download a good freeware, shareware or evaluation copy of a ->xwindows client? thanks a lot in advance, cheers I have used both the freeware time limited demo and paid for the full version from http://www.starnet.com/ They both work quite well. Roger Isaacson risaacson@physics.ucsd.edu UCSD Physics Dept PH 619-534-2505 9500 GILMAN DRIVE FAX 619-822-0007 LA JOLLA CA 92093-0319 From owner-software@net.bio.net Mon Aug 10 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: sales@biblioscape.com Newsgroups: bionet.software Subject: Re: Endnote writer for the PC Date: Tue, 11 Aug 1998 00:37:31 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 23 Message-ID: <6qo3ob$7o3$1@nnrp1.dejanews.com> References: <35B9FBEB.20A6@magnus.acs.ohio-state.edu> NNTP-Posting-Host: 128.192.2.200 X-Article-Creation-Date: Tue Aug 11 00:37:31 1998 GMT X-Http-User-Agent: Mozilla/4.04 [en] (WinNT; I) Hi Arffaan, If you use Windows 95, 98, or NT4, you can try a bibliographic software called Biblioscape. You can download a fully functional trial copy at www.biblioscape.com Paul In article <35B9FBEB.20A6@magnus.acs.ohio-state.edu>, arfaan Rampersaud wrote: > When I had my macintosh there was a program that allowed me to save > references from the Reference Update software program to the Endnotes > bibliographic software. I believe the program was called Endnote > Writer. I am now using a PC and would like to find out if something > similar is available for Windows. > > Thanks > > Arfaan Rampersaud > -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-software@net.bio.net Mon Aug 10 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!woodstock.news.demon.net!demon!dispose.news.demon.net!demon!delos!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: xwindows clinet Date: 11 Aug 1998 12:32:45 GMT Organization: University of Cambridge Message-ID: <6qpdld$fub$1@pegasus.csx.cam.ac.uk> References: <35C4A854.F282DE16@accefyn.org.co> <35cfb338.343877@news-server> NNTP-Posting-Host: mole.bio.cam.ac.uk Lines: 34 In article , Fergus Doherty wrote: >(Since then I have been able to buy White Pine's eXodus for MacOS which is >very good. Indeed it is, but it has security problems (it allows all users on the host to which you are making an XDMCP query to access your X display, and there is no way to stop it doing this). MacX is also insecure. I do not know of any Mac X server which does not have this sort of problem, yet. On PCs, Exceed is similarly configured unsecurely by default, although you can configure it not to allow xhost type authentication. This is a serious worry at the moment, since machines in UK universities are being actively probed by hackers for insecure X servers. If you want to do X, I would suggest either using Exceed, or (better still) use a UNIX box; either a genuine workstation or a Linux box set up as an X terminal, running as little other software as possible, so that it doesn't become a target for hackers itself. Tim. -- -------------------------------------------------------------------------- Dr T J R Cutts Tel: +44 1223 333596 Dept. of Biochemistry, 80 Tennis Court Rd. Cambridge, CB2 1GA, UK From owner-software@net.bio.net Mon Aug 10 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!bofh.vszbr.cz!pegasus.csx.cam.ac.uk!server1.netnews.ja.net!news.nott.ac.uk!Fergus.Doherty From: Fergus.Doherty@nottingham.ac.uk (Fergus Doherty) Newsgroups: bionet.software Subject: Re: xwindows clinet Date: Tue, 11 Aug 1998 12:59:39 +0100 Organization: Nottingham University Lines: 26 Message-ID: References: <35C4A854.F282DE16@accefyn.org.co> <35cfb338.343877@news-server> NNTP-Posting-Host: wmbpm8.nottingham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 > On 2 Aug 1998 10:58:18 -0700, acad@ACCEFYN.ORG.CO (Alexander Garcia) > wrote: > > ->Where can I download a good freeware, shareware or evaluation copy > of a > ->xwindows client? thanks a lot in advance, cheers > Microimages do a passable free (not time limited) X-Window app for MacOS and Windows: http://tnt.microimages.com/freestuf/mix/ I have used it with GCG SeqLab. On a Mac I found I had to telnet to the client first to set up the X-Window session (ie no XDM), but apart from that it was OK - well brilliant for free! (Since then I have been able to buy White Pine's eXodus for MacOS which is very good. -- Fergus Doherty, Dept Biochemistry, Nottingham University, Fergus.Doherty@nottingham.ac.uk 0115 970 9366 (74-41366 internal) From owner-software@net.bio.net Mon Aug 10 23:00:00 1998 Path: biosci!angis.usyd.edu.au!tim From: tim@angis.usyd.edu.au (Tim Littlejohn) Newsgroups: bionet.software Subject: Re: Translation of protein sequence to nucleotide sequence Date: 11 Aug 1998 04:58:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 95 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199808111125.HAA12978@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net Francis has just been working too hard that's all! The only one I know of off the top of my head is GCG's backtranslate. Cheers, Tim On 11 Aug 1998 francis@ncbi.nlm.nih.gov wrote: > sorry Tony, you are right, I totally missed your point .. (as Tim > Littlejohn also pointed out to me) ...Your posting was not ambiguious, > it was I who missread it ... sorry, I have no suggestions, but others > may have ... > > regards, > > f. > > -- > | B.F. Francis Ouellette > | GenBank Coordinator > | > | francis@ncbi.nlm.nih.gov > > > > From mcbaet@mcbsgs1.imcb.nus.edu.sg Tue Aug 11 01:08:09 1998 > > X-Sender: mcbaet@imcb.nus.edu.sg > > Date: Tue, 11 Aug 1998 13:08:53 +0800 > > To: francis@ncbi.nlm.nih.gov > > From: Anthony Ting > > Subject: Re: Translation of protein sequence to nucleotide sequence > > > > Dear Francis, > > > > Thanks for the prompt reply. While ORF Finder is a nice program. It does > > the opposite of what I want. I already have a protein sequence, what I > > want to do is convert to nucleotide sequence given a specific codon usage > > table. I'm sorry if my original posting was ambiguious. If you have any > > suggestions, I'd really appreciate it. Otherwise, I'm spending the next > > few days doing it manually. > > > > thanks again, > > > > Tony > > > > > > > > At 11:53 PM 8/10/98 -0400, you wrote: > > > > > >> From: mcbaet@MCBSGS1.IMCB.NUS.EDU.SG (Anthony Ting) > > > > > >=-> Is anyone aware of a program that translate a protein > > >=-> sequence into > > >=-> a nucleotide sequence given a specific codon usage table? > > > > > >Dear Anthony Ting, > > > > > >have a look ORF Finder at: > > > > > >http://www.ncbi.nlm.nih.gov/gorf/gorf.html > > > > > >I think it will do what you want (and a little bit more :-) > > > > > >cheers, > > > > > >francis > > > > > >-- > > >| B.F. Francis Ouellette > > >| GenBank Coordinator > > >| > > >| francis@ncbi.nlm.nih.gov > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------- > > Anthony Ting, PhD phone: 65-874-7846 > > Institute of Molecular and Cell Biology fax: 65-779-1117 > > 30 Medical Drive > > Singapore 117609 > > > > -------------------------------------------------------------------------- | ANGIS- The Australian National Genomic Information Service | | http://www.angis.org.au email: tim@angis.org.au | | Phone Toll Free: 1 800 728 028 FAX: 61-2-9351 1878 | -------------------------------------------------------------------------- From owner-software@net.bio.net Mon Aug 10 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!Cabal.CESspool!bofh.vszbr.cz!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Michele Clamp Newsgroups: bionet.software Subject: Re: Translation of protein sequence to nucleotide sequence Date: 11 Aug 1998 12:34:28 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 26 Message-ID: References: <35CEA9D3.AE38C855@imcb.nus.edu.sg> NNTP-Posting-Host: speed.ebi.ac.uk X-Newsreader: Gnus v5.5/Emacs 20.2 mcbaet@MCBSGS1.IMCB.NUS.EDU.SG (Anthony Ting) writes: > Hi there, > > Is anyone aware of a program that translate a protein sequence into > a nucleotide sequence given a specific codon usage table? > The only thing I can think of is GCG's backtranslate which will give you the most and least probable DNA sequence. On a similar note and while I'm thinking of it does anyone out there know of something that will compare 2 protein sequences at the DNA level and give you the most likely DNA alignment. I'd find this useful for finding possible undetected frame shift errors in multiple alignments. Thinking about it this is trickier than I first imagined and not just a quick perl hack. M. -- Dr Michele Clamp , EMBL-European Bioinformatics Institute Hinxton, Cambs CB10 1SD, email : michele@ebi.ac.uk UK Tel: 01223 494682 Fax: 01223 494468 From owner-software@net.bio.net Mon Aug 10 23:00:00 1998 Path: biosci!NCBI.NLM.NIH.GOV!francis From: francis@NCBI.NLM.NIH.GOV Newsgroups: bionet.software Subject: Re: Translation of protein sequence to nucleotide sequence Date: 10 Aug 1998 20:56:26 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <199808110353.XAA12549@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net > From: mcbaet@MCBSGS1.IMCB.NUS.EDU.SG (Anthony Ting) =-> Is anyone aware of a program that translate a protein =-> sequence into =-> a nucleotide sequence given a specific codon usage table? Dear Anthony Ting, have a look ORF Finder at: http://www.ncbi.nlm.nih.gov/gorf/gorf.html I think it will do what you want (and a little bit more :-) cheers, francis -- | B.F. Francis Ouellette | GenBank Coordinator | | francis@ncbi.nlm.nih.gov From owner-software@net.bio.net Mon Aug 10 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.concentric.net!priori!news.idt.net!nntp.giganews.com!cyclone.swbell.net!news.pbi.net!not-for-mail From: Ron Kagan Newsgroups: bionet.software Subject: Multiplex PCR Primer Design Program? Date: Tue, 11 Aug 1998 10:13:02 -0700 Organization: Quest Diagnostics Lines: 9 Message-ID: <35D07B9E.7D1A23A5@pacbell.net> NNTP-Posting-Host: ppp-207-214-243-168.irvn11.pacbell.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; U) Does anyone know of a program for designing primers for multiplex PCR amplification of several different templates in one reaction? Thanks, Ron Kagan Quest Diagnostics qdbio@pacbell.net From owner-software@net.bio.net Tue Aug 11 23:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!Supernews60!supernews.com!uunet!in4.uu.net!whowhere.com!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: Translation of protein sequence to nucleotide sequence Date: 12 Aug 1998 15:23:56 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 26 Message-ID: <6qsc2c$hii@gap.cco.caltech.edu> References: <35CEA9D3.AE38C855@imcb.nus.edu.sg> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu In article , Michele Clamp writes: >mcbaet@MCBSGS1.IMCB.NUS.EDU.SG (Anthony Ting) writes: > >On a similar note and while I'm thinking of it does anyone out there >know of something that will compare 2 protein sequences at the DNA >level and give you the most likely DNA alignment. I'd find this >useful for finding possible undetected frame shift errors in multiple >alignments. > The only tool that I know of which is even close is GCG's FRAMEALIGN. It aligns a protein to DNA, allowing for frameshifts. It is the only safe way to go when aligning to an EST, since they have a very, very high rate of frameshifts and other errors. However, it assumes that the protein sequence in the comparison is fully in the correct frame, which might not be true if, for instance, all you had to start with is a collection of ESTs. Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech ************************************************************************** * RIP VMS * ************************************************************************** From owner-software@net.bio.net Tue Aug 11 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.nyu.edu!btnet-peer!btnet!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.ox.ac.uk!not-for-mail From: "Stuart Montgomery" Newsgroups: bionet.software Subject: I am looking for a Oligo Data base Date: Wed, 12 Aug 1998 09:55:23 +0100 Organization: Oxford University Lines: 6 Message-ID: <6qrleh$ld5$1@news.ox.ac.uk> NNTP-Posting-Host: cfgnt2.zoo.ox.ac.uk X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Hi Does anyone have any suggestions which oligo database to use? Thanks Stuart Montgomery From owner-software@net.bio.net Tue Aug 11 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!newsfeed.nacamar.de!univ-lyon1.fr!jussieu.fr!univ-lille1.fr!u-strasbg.fr!news From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: Help: dbwatcher.linux Date: 12 Aug 1998 08:55:15 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 24 Message-ID: <6qrl9j$cg6@news.u-strasbg.fr> References: <6qrft9$tea@majestix.uni-muenster.de> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.8 Mail-Copies-To: never To: "Ralf Spenneberg" [Posted and mailed] In article <6qrft9$tea@majestix.uni-muenster.de>, "Ralf Spenneberg" writes: > Maybe anybody out there can shed some light? The answer should be there : http://www-igbmc.u-strasbg.fr/BioInfo/LocalDoc/DBWatcher/TroubleShooting.html Please let me know if it works. Fred is out for 3 weeks, but I can try to help you. Roughly, your job directory is unreadable by dbwatcher, check permissions. François. P.S.: The HTML doc is pretty good, please follow : http://www-igbmc.u-strasbg.fr/BioInfo/LocalDoc/DBWatcher/ -- 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 Tue Aug 11 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!london-news-feed1.bbnplanet.com!news.bbnplanet.com!diablo.theplanet.net!news-lond.gip.net!news.gsl.net!gip.net!news-fra.maz.net!news-fra1.dfn.de!news-koe1.dfn.de!uni-muenster.de!news From: "Ralf Spenneberg" Newsgroups: bionet.software Subject: Help: dbwatcher.linux Date: Wed, 12 Aug 1998 09:24:10 +0100 Organization: Inst. for Med. Biochemistry Lines: 31 Sender: "Ralf Spenneberg" Message-ID: <6qrft9$tea@majestix.uni-muenster.de> NNTP-Posting-Host: imbmac01.uni-muenster.de Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express for Macintosh - 4.01 (295) Hi, I try to setup dbwatcher on a linux machine using the linux executable. But the only response I am getting is: Job 'Annexin' : 'blastp' on database 'NCBI:month' with parameters 'V=250 B=250 -filter seg' Results with P < 1.00E-03 sent to spenneb@uni-muenster.de. Connection to server OK Information about remote databases collected ******* Error! Database 'NCBI:month' was not found! Well... It seems there isn't any more job to do. See you soon. Maybe anybody out there can shed some light? Ralf Ralf Spenneberg Center for molecular biology of inflammation Von Esmarchstr 56, 48149 Muenster, Germany Tel.: ++49 (0)251 8352126 Fax: 8356748 From owner-software@net.bio.net Tue Aug 11 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!oleane!jussieu.fr!univ-lille1.fr!u-strasbg.fr!news From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: Sequence alignment package for LaTeX? Date: 12 Aug 1998 11:42:06 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 21 Message-ID: <6qrv2e$cg6@news.u-strasbg.fr> References: 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 0.9.8 Mail-Copies-To: never In article , Ian Holmes writes: > Hi, > > Does anyone happen to know of a package for displaying sequence > alignments in LaTex? I use alscript and then import postscript output. If I remember well, you should use alscript standard output (not the ps file) to define the bounding box to be able to include the graphics properly (like you probably do with XFig). I didn't do it for a year because lot of editors are asking for Mac or PC files. 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 Tue Aug 11 23:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!interpath.net!news-relay.ncren.net!ussun2n!news@ussun2n.glaxo.com From: Sandra Marina Newsgroups: bionet.software Subject: care about anything? Date: Wed, 12 Aug 1998 17:29:25 +0100 Organization: United Earth Alliance Lines: 19 Message-ID: <35D1C2E5.1144E6D6@nospam.uea.net> NNTP-Posting-Host: 147.184.168.172 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (WinNT; I) This is for those you you that care about the future. An organisation called the United Earth Alliance needs you help. We need you to volunteer for our agencies and to bring with you, your skills and opinions. The UEA is an international organisation, that carries out scientific research, aid relief and tackles social and environmental problems through out the world. If you think you can help, then please visit our website to find out more. http://www.uea.net Thank you for you time. GCA -- United Earth Alliance Small Step. Right Direction. http://www.uea.net From owner-software@net.bio.net Tue Aug 11 23:00:00 1998 Path: biosci!INDIGO14.CARB.NIST.GOV!glab From: glab@INDIGO14.CARB.NIST.GOV (Gilson Job Response) Newsgroups: bionet.software Subject: Bioinformatics/Chemoinformatics research positions in Maryland Date: 12 Aug 1998 10:21:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <199808121717.NAA20559@indigo14.carb.nist.gov> NNTP-Posting-Host: net.bio.net
BIOINFORMATICS/CHEMOINFORMATICS POSITIONS

CENTER FOR ADVANCED RESEARCH IN BIOTECHNOLOGY (CARB)

Rockville, Maryland

One programmer position and one graduate student or postdoctoral position will soon become available in a project to develop a new web-accessible database. The database will contain experimental data -- thermodynamics, structural data, etc. -- on molecular recognition complexes from biology and chemistry. This database is expected to be of value to researchers in both academia and industry. Funding is from NSF and NIST.

To work on the project, you should have knowledge of database design and the WWW, as well as the scientific background to understand the data and its applications. To apply, please send email with description of your interests and a CV or resume to gilson_lab@carb.nist.gov.

CARB is a research and training institute about 20 miles from DC. Research here focuses on the structure and function of proteins and other biomolecules. CARB is an EEO/AA Employer. Women and minority candidates are encouraged to apply. From owner-software@net.bio.net Tue Aug 11 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!news1.best.com!newshub.sdsu.edu!franklin.ljcrf.edu!not-for-mail From: greg@franklin.burnham-inst.org () Newsgroups: bionet.software Subject: FTP site for Sippl's proFIT? Date: 12 Aug 1998 15:45:29 GMT Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE Lines: 23 Message-ID: <6qsdap$kr0$1@franklin.ljcrf.edu> NNTP-Posting-Host: franklin.ljcrf.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Hi; I have been asked to install the proFIT fold prediction software. But I can't see anywhere either a reference for buying a commercial version or a place to FTP the academic version from. Can anyone help? (I've already been through to Kingsbeach software homepage, which is pretty useless in providing any kind of information). Thanks for any help. Greg -- ***************************************** Computational Biology Group The Burnham Institute (formerly La Jolla Cancer Research Inst.) 12901 North Torrey Pines road La Jolla CA92037 Phone:(619) 646 3103 Email: greg@franklin.ljcrf.edu http://franklin.ljcrf.edu/greg http://www.greg.com/ ***************************************** From owner-software@net.bio.net Tue Aug 11 23:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!europa.clark.net!194.162.162.196!newsfeed.nacamar.de!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!scarp.sanger.ac.uk!ihh From: Ian Holmes Newsgroups: bionet.software Subject: Sequence alignment package for LaTeX? Date: Wed, 12 Aug 1998 11:26:16 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 9 Message-ID: NNTP-Posting-Host: scarp.sanger.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Does anyone happen to know of a package for displaying sequence alignments in LaTex? Cheers, Ian Holmes The Sanger Centre From owner-software@net.bio.net Wed Aug 12 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!newsfeed.internetmci.com!158.43.192.17!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!jkb From: jkb@mrc-lmb.cam.ac.uk (James Bonfield) Newsgroups: bionet.software Subject: Re: Translation of protein sequence to nucleotide sequence Date: 13 Aug 1998 08:26:01 GMT Organization: MRC Laboratory of Molecular Biology, Cambridge UK Lines: 92 Distribution: world Message-ID: <6qu7up$7us$1@pegasus.csx.cam.ac.uk> References: <35CEA9D3.AE38C855@imcb.nus.edu.sg> NNTP-Posting-Host: alf2.mrc-lmb.cam.ac.uk In article <35CEA9D3.AE38C855@imcb.nus.edu.sg> mcbaet@MCBSGS1.IMCB.NUS.EDU.SG (Anthony Ting) writes: > Is anyone aware of a program that translate a protein sequence into >a nucleotide sequence given a specific codon usage table? The "pip" program (also xpip) in the Staden Package can manage this. It is option "27 = Back translate to dna". Be sure to type "d27" rather than just "27", for the addition dialogue questions, or when using xpip have the "execute with dialogue" button enabled. Eg: ? Menu or option number=m1 General menu 0 = List of menus 3 = Read a new sequence 4 = Redefine active region 5 = List a sequence 6 = List a text file 7 = Direct output to disk 8 = Write active region to disk 9 = Edit the sequence 17 = Short sequence search 18 = Compare a sequence 19 = Compare a sequence using a score matrix 27 = Back translate to dna ? Menu or option number=d27 Back translate to dna ? No codon preference (y/n) (y) = n ? Codon table file name= I've included a copy of the help for the dialogue in this article. Please also see the staden package web pages for more details (in my .sig). James ============================================================================= Help on 'Back translate to dna' (option 27) This routine back translates protein sequences into DNA using the standard genetic code. The level of redundancy can be plotted and the backtranslation saved to a file. The translation can use either the IUB symbols shown below, or a set of codon preferences. If a set of codon preferences are used they must conform to the format of codon tables produced by the nucleotide analysis program, and the back translation will contain the favoured codons. If there is no favoured codon the IUB symbols will be employed. The window length for plotting the redundancy is in codons. The program will plot the redundancy along the sequence and hence can be used to find the best sequences to use as primers. Note that the program plots the inverse, and so the higher the plot the LESS redundant the sequence. For primers look for peaks rather than troughs. The DNA sequence can be saved to a file and analysed using the nucleotide analysis program. Depending on the application it is often useful to produce a back translation using both a table of codon preferences and one using the IUB symbols. This is because the restriction enzyme search program can distinguish between definite and possible cuts in the sequence. These matches are what the program terms "definite matches" and are ones in which the specification of the recognition sequence corresponds exactly to that of the back translation. The program will also find what it terms "possible matches" which are ones that depend on the particular codons chosen for each amino acid. These are sites at which recognition sequences could be engineered to produce a cut in the DNA without changing the amino acid, but which are not necessarily found in the original sequence. NC-IUB SYMBOLS A,C,G,T R (A,R) 'puRine' Y (T,C) 'pYrimidine' W (A,T) 'Weak' S (C,G) 'Strong' M (A,C) 'aMino' K (G,T) 'Keto' H (A,T,C) 'not G' B (G,C,T) 'not A' V (G,A,C) 'not T' D (G,A,T) 'not C' N (G,A,C,T) 'aNy' -- James Bonfield (jkb@mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556 Medical Research Council - Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/ From owner-software@net.bio.net Wed Aug 12 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!204.127.161.4!wn4feed!worldnet.att.net!135.173.83.225!attworldnet!newsadm From: Abhay Kini Newsgroups: bionet.software Subject: Predicting transmembrane sequences Date: 13 Aug 1998 20:56:28 GMT Organization: Purdue University Lines: 10 Message-ID: <35D35123.3C0D7596@worldnet.att.net> Reply-To: kinis@cheerful.com NNTP-Posting-Host: 12.72.192.240 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (Win95; U) I am looking for a software that would predict the transmembrane sequences in a receptor. Some of the ones available on the web do not seem to work. Any suggesstions..? Thanx Abhay From owner-software@net.bio.net Wed Aug 12 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!news-nyc.telia.net!newsfeed.nyu.edu!news.nyu.edu!mcrcr1.med.nyu.edu!user From: browns02@mcrcr.med.nyu.edu (Stuart Brown) Newsgroups: bionet.software Subject: Alignment of DNA with protein Date: Thu, 13 Aug 1998 13:30:52 -0500 Organization: NYU Med Center Lines: 51 Message-ID: References: <35CEA9D3.AE38C855@imcb.nus.edu.sg> <6qsc2c$hii@gap.cco.caltech.edu> NNTP-Posting-Host: mcrcr1.med.nyu.edu X-Trace: news.nyu.edu 903029151 2606 (None) 128.122.135.49 X-Complaints-To: usenet@news.nyu.edu In article <6qsc2c$hii@gap.cco.caltech.edu>, mathog@seqaxp.bio.caltech.edu wrote: > In article , Michele Clamp writes: > >mcbaet@MCBSGS1.IMCB.NUS.EDU.SG (Anthony Ting) writes: > > > >On a similar note and while I'm thinking of it does anyone out there > >know of something that will compare 2 protein sequences at the DNA > >level and give you the most likely DNA alignment. I'd find this > >useful for finding possible undetected frame shift errors in multiple > >alignments. > > > > The only tool that I know of which is even close is GCG's FRAMEALIGN. It > aligns a protein to DNA, allowing for frameshifts. It is the only safe way > to go when aligning to an EST, since they have a very, very high rate of > frameshifts and other errors. However, it assumes that the protein > sequence in the comparison is fully in the correct frame, which might not > be true if, for instance, all you had to start with is a collection of > ESTs. > > Regards, > David Mathog > mathog@seqaxp.bio.caltech.edu I'm not sure if this is exactly what you have in mind, but the TFASTX3 program in Pearson's FASTA 3.0 package compares a protein to a DNA sequence, translating the DNA in all reading frames and allowing for frameshift mutations. It is a hell of a lot faster than GCG's FRAMEALIGN and it is free. I am working on a similar problem and would appreciate all opinions. I want to add DNA sequences to a protein alignment. Turn the protein sequence into 3-letter code and match up the corresponding DNA codons for each protein in the multiple alignment. I want the DNA seqs. to follow the gaps that have been introduced in the protein alignment, but in the case of introns, the entire protein alignment would be gapped across the DNA sequences. This whole process needs to be fairly quick and easy since we want to make a lot of these hybrid DNA/protein alignments and use them as the starting point for other analyses. Cheers ‹ Stuart Brown -- Kim B. Foglia WriteDesign The Working Moms' Internet Refuge From owner-software@net.bio.net Wed Aug 12 23:00:00 1998 Path: biosci!news.stanford.edu!nntp.cs.ubc.ca!newsfeed.direct.ca!news-peer.sprintlink.net!news-nysernet-5.sprintlink.net!news.sprintlink.net!128.122.253.90!newsfeed.nyu.edu!news.nyu.edu!mcrcr1.med.nyu.edu!user From: browns02@mcrcr.med.nyu.edu (Stuart Brown) Newsgroups: bionet.software Subject: Re: Multiplex PCR Primer Design Program? Date: Thu, 13 Aug 1998 13:33:36 -0500 Organization: NYU Med Center Lines: 26 Message-ID: References: <35D07B9E.7D1A23A5@pacbell.net> NNTP-Posting-Host: mcrcr1.med.nyu.edu X-Trace: news.nyu.edu 903029312 2606 (None) 128.122.135.49 X-Complaints-To: usenet@news.nyu.edu In article <35D07B9E.7D1A23A5@pacbell.net>, Ron Kagan wrote: > Does anyone know of a program for designing primers for multiplex PCR > amplification of several different templates in one reaction? > > Thanks, > > Ron Kagan > Quest Diagnostics > qdbio@pacbell.net RightPrimer has functions to do this. I won't swear as to how well it works though. RightPrimer is a commercial program distributed by BioDisk Software P.O. Box 26447 San Francisco, CA 94126 U.S.A. Voice: (800) 664-DISK/(415) 951-9031 Fax: (415) 951-0102 Internet: sales@biodisk.com -- Stuart M. Brown Bioinformatics Consultant NYU Medical Center, 550 First Ave, NY, NY From owner-software@net.bio.net Wed Aug 12 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!newsfeed.nacamar.de!nntp.news.xara.net!xara.net!server6.netnews.ja.net!server4.netnews.ja.net!server2.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!scarp.sanger.ac.uk!ihh From: Ian Holmes Newsgroups: bionet.software Subject: Re: Translation of protein sequence to nucleotide sequence Date: Thu, 13 Aug 1998 16:51:06 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 14 Message-ID: References: <35CEA9D3.AE38C855@imcb.nus.edu.sg> <6qsc2c$hii@gap.cco.caltech.edu> NNTP-Posting-Host: scarp.sanger.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <6qsc2c$hii@gap.cco.caltech.edu> Sywise in the latest Genewise release does this I think. Go to http://www.sanger.ac.uk/Users/birney/ & follow Wise* links. Alternatively the package that Sywise is written in - Dynamite - allows flexible design of finite state automata. If Ewan Birney hasn't already written an automaton to align protein at the DNA level then it would be very easy to do so, or mail him on birney@sanger.ac.uk Ian From owner-software@net.bio.net Wed Aug 12 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!oleane!jussieu.fr!saphir.jouy.inra.fr!lindenb From: lindenb@jouy.inra.fr (Pierre Lindenbaum) Newsgroups: bionet.software Subject: Re: [ANNOUNCE] CloneIt Finding cloning strategies Date: 13 Aug 1998 10:20:10 GMT Organization: INRA Lines: 1 Message-ID: <6quekq$jdv$1@saphir.jouy.inra.fr> References: <6que9j$ja7$1@saphir.jouy.inra.fr> NNTP-Posting-Host: biotec.jouy.inra.fr X-Newsreader: TIN [version 1.2 PL2] test From owner-software@net.bio.net Wed Aug 12 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!oleane!pasteur.fr!jussieu.fr!saphir.jouy.inra.fr!lindenb From: lindenb@jouy.inra.fr (Pierre Lindenbaum) Newsgroups: bionet.software Subject: [ANNOUNCE] CloneIt Finding cloning strategies Date: 13 Aug 1998 10:14:11 GMT Organization: INRA Lines: 234 Message-ID: <6que9j$ja7$1@saphir.jouy.inra.fr> NNTP-Posting-Host: biotec.jouy.inra.fr X-Newsreader: TIN [version 1.2 PL2] CLONEIT AN ANSI-C PROGRAM FINDING SUB-CLONING STRATEGIES, IN-FRAME DELETIONS AND FRAMESHIFTS USING RESTRICTION ENZYMES AND DNA POLYMERASES. What is CloneIt ? Molecular biologists often have to sub-clone plasmidic vectors: a DNA plasmid is cleaved and ligated with an exogen DNA fragment previously excised from an other plasmid. The necessary cuts are made by restriction enzymes which then must be carefully choosen in order to minimize the steps required to obtain the desired molecule. During the selection of those enzymes, the main difficulties encountered come from: the knowldege of: + the enzymes' characteristics + the localization of the cuts within the sequence + the complementarity between the protuding ends + the possible self ligation of the vector + the use of modifying DNA polymerases that generate blunt ends + the constraint to clone the insert in-frame with a vector sequence + the use of partial digestions + the creation of a stop codon after the ligation. This exercise takes a long time even with a computorized help of the classic DNA analysis softwares that only help the user by localizing restriction sites that are present a few times in a plasmid sequence. All combinations cannot be humanly checked by the scientist, so a simple cloning strategy can be missed by the experimenter. We developed a program that quickly finds in-frame deletions using restriction enzymes and frameshifts (using digestion, fill-in and ligation) in a plasmid sequence, Then, as the main functions and procedures were being developed, we have extended the capacities of the program to find strategies to sub-clone a fragment from a plasmid to another vector while still controling the problems described above. This program is not an expert system, as it does not "learn" the logical steps accomplished by the biologist and it does not have to be accompanied in its search: it just runs an algorithm that explores all the possible enzymes combinations that could be used to clone the molecules. This program called CloneIt , written in ANSI C, provides a useful aid for any molecular biologist who wants to quickly find sub-cloning, in-frame deletions, frameshifts strategies, which would otherwise be difficult to discover. This program handle parameters such as + usage of a phosphatase (CIP) + usage of modifying polymerases that blunt overhanged ends + partial digestions + 5' or/and 3' in-frame ligation + digestion post ligation + digestion to direct insert + detection of stop codon after ligation + Compare 2 sequences from the point of view of restriction sites. + Display a restriction map. + Translation of restriction enzymes databases. + Management of large cloning projects. CloneIt source code The source code is freely available at http://locus.jouy.inra.fr/soft/cloneit/clonit.html ------------------------------------------------------------------------------ Samples ------------------------------------------------------------------------------ Restriction Map .............................................................................. SACI SALI ECORI : hincii styi acsi : acci ECO52I NCOI alwi : ECL136II eaei bstdsi xhoii : bsp1286i bsh1285i MSCI xmni BAMHI : banii : NOTI eaei ecorv : vspi alwi : alw21i : HINDIII: : : : : : :: : : : : :: TGGCCATGGATATCGGAATTAATTCGGATCCGAATTCGAGCTCCGTCGACAAGCTTGCGGCCGCA \ 5266 ¥ ¥ ¥ ¥ ¥ ¥ ¥ \ ACCGGTACCTATAGCCTTAATTAAGCCTAGGCTTAAGCTCGAGGCAGCTGTTCGAACGCCGGCGT \ 5330 T P T :I S E :L I R::I R: I R: A P :S T :S L :R P H -> :A :M D: I G :I: N S D: P N S S S V: D K: L A::A A L -> : H: G Y R N: * F G :S E :F E :L R R Q A C G: R T -> : P: V $ L R: L * A :$ A :* A :R P L Q E F A: P T .............................................................................. Finding in-frame deletions .............................................................................. CloneIt has found an in-frame deletion: Digest INSERT with Bcl I [t^gatca] (1427) and PstI [CTGCA^G] (3611). 5' --TG.TAT./GAT.C AG.GTT.CTT.ACT.G-- --CG.ACC. TGC.A/GG.CAT.GCA.AGC.T-- 3' 3' --AC.ATA. CTA.G/TC.CAA.GAA.TGA.C-- --GC.TGG./ACG.T CC.GTA.CGT.TCG.A-- 5' NH2 Y D Q V L T E -- -- T C R H A S F .COOH Treat with T4 DNA polymerase. Cloning boxes boundaries :[880-1155] [3359-3634]. Original: 5' ================================================ 3' Deletion: 5' =========......................................= 3' Equivalent to a deletion of 728 amino acids [79 %] Digestion post-ligation: BamHI Sal I Acc I Nsi I . The first stop codon detected AFTER the PstI site (3611) is localized at position 3639 on insert. Translated truncated sequence:... NSSSVPGAIKGSMAYRKRGARREANINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVV TDSQEEIKIADEVKKSTKEESKQLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLE DIKPEQAKKQTKLFRIFEPRQLPIYRANGEKELRNRTYTKLKKDTLPGDYDVREYFLNLY DR---------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --HASFCS... .............................................................................. Finding frameshifts in INSERT. .............................................................................. CloneIt has found an Enzyme that could induce frameshift. Digest INSERT with AccI [gt^mkac] (1659). 5' --.ATC.AGT.//AT A.CAC.ATA.AAT.GAT-- 3' 3' --.TAG.TCA. TA//T.GTG.TAT.TTA.CTA-- 5' NH2 I S I H I N D .COOH Treat with Klenow DNA polymerase. Beware : AccI [1 partial site] . After digestion, fill-in and ligation: 5' .ATC.AGT.ATA.TAC.ACA.TAA.ATG 3' 3' .TAG.TCA.TAT.ATG.TGT.ATT.TAC 5' NH2 I S I Y T * M COOH ¥ FrameShift (+ 2) ¥ 2 bases Added. ¥ Site is NOT reconstitued after ligation. ¥ [51 %] percentage of Insert. FIGURE: ========================= | (+2) =========================== Translated sequence:...EFELGTRGSMATFKDACYHYKRLNKLNSLVLKLGANDETRPAPMTKYKGTCL YTNLTYCRGCALYHVCQTCSQYNRCFLDEEPHLLRMRTFKDVVTKEDIEGLLTMYETLFPINEKLVNKFINSVKQ EYLLETYNHLLMPITLQALTINLEDNVYYIFGYYDCMEHENQTPFQFINLLEKYDKLLLDDRNFHRMSHLPVILQ RYFSKSRFLSKGKKRLSRSDFSDNLMEDRHSPTSLMQVVRNCISiyT*... .............................................................................. SubCloning .............................................................................. CloneIt V1.0 has found a solution: Digest VECTOR with EcoRI [G^AATTC] (878) and Sal I [g^tcgac] (894). 5' --G.CCG.G/AA.TT C.CCG.GGG.ATC.CG/T.CGA. CCT.GCA.GCC.AAG-- 3' 3' --C.GGC.C TT.AA/G.GGC.CCC.TAG.GC A.GCT./GGA.CGT.CGG.TTC-- 5' NH2 P E F P G I R R P A A K .COOH Digest first with EcoRI .Then treat with Klenow DNA polymerase.Finally digest with Sal I . Digest INSERT with Sca I [AGT^ACT] (1034) and Sal I [g^tcgac] (3605). 5' --AT.AAA.GT/ A.CTT.TCA.AAG.AAA.G-- --TA.GAG./TCG.A CC.TGC.AGG.CAT.G-- 3' 3' --TA.TTT.CA/ T.GAA.AGT.TTC.TTT.C-- --AT.CTC. AGC.T/GG.ACG.TCC.GTA.C-- 3' NH2 K V L S K K E -- -- E S T C R H A .COOH Treat with T4 DNA polymerase. Sites wil be in frame ligated in 5'. The first stop codon