From owner-software@net.bio.net Mon Feb 01 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!oleane!jussieu.fr!moka.ccr.jussieu.fr!not-for-mail From: ptitjean@ccr.jussieu.fr (Michel PETITJEAN) Newsgroups: bionet.software Subject: minimal sphere Date: 2 Feb 1999 15:42:45 +0100 Organization: CCR - Universites Paris VI/VII - Paris - France Lines: 15 Message-ID: <7972t5$59lq@moka.ccr.jussieu.fr> NNTP-Posting-Host: moka.ccr.jussieu.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Subj: minimal sphere A colleague told me recently that it should be useful to have a programme computing the minimal sphere containing a molecule, together with various shape coefficients. I have done it. Binaries are available for DEC-alpha (VMS and unix), RS6000 serie (and SP2) CRAY Y and J90, SGI O2 (and various mips1 to mips4). Interested people should email me, without forgetting to tell which computer is used. Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, ESA 7086) ptitjean@ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 01 44 27 48 57 75005 Paris, France. FAX : +33 01 45 84 98 25 From owner-software@net.bio.net Mon Feb 01 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server6.netnews.ja.net!st-and!etd From: etd@bigfoot.com (Edwin ten Dam) Newsgroups: bionet.software Subject: Re: DNA sequence analysis for Mac Date: Tue, 02 Feb 1999 14:58:29 +0000 Organization: School of Biomedical Sciences - University of St Andrews Lines: 24 Message-ID: References: <36B31D13.7366F38E@icr.ac.uk> <36B5FAE3.875ECC6E@chollian.net> NNTP-Posting-Host: bmsmac-mdr1.st-and.ac.uk X-Newsreader: MT-NewsWatcher 2.4.4 X-Face: -P+89ASh_wrs;AUGm`!l[}/o-lyK}5W.gq\fkJ{#d6Gu,hWrZNz::iMm5PJb} __A96]-LUrl)X=uF=V|\3-\9/sXvBs/H In article <36B5FAE3.875ECC6E@chollian.net>, Senovia von Perle wrote: >There are several softwares for DNA sequence analysis... >MacDNAsis by Hitachi software... >MacVector by Oxford... >Sequencher... >MacStar... Macvector is very nice. The price is rediculous though: A very outrageous 1800 pounds! I can't see many University labs forking out that sort of money. Why there isn't an academic discount I can't understand. cheers, Edwin -- Edwin ten Dam etd@bigfoot.com School of Biomedical Sciences - University of St Andrews Biomolecular Sciences Bldng, North Haugh, St Andrews, KY16 9ST U.K. Phone: +44 1334 463404 - Fax: +44 1334 462595 From owner-software@net.bio.net Mon Feb 01 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!logbridge.uoregon.edu!feed1.news.rcn.net!rcn!newsfeed.cwix.com!194.72.7.126!btnet-peer!btnet!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.staden,bionet.software Subject: Staden Pkg 1999.0 - Free to academics Date: 2 Feb 1999 18:36:28 GMT Organization: MRC Laboratory of Molecular Biology, Cambridge UK Lines: 55 Distribution: world Message-ID: <797gjc$70l$1@pegasus.csx.cam.ac.uk> NNTP-Posting-Host: alf2.mrc-lmb.cam.ac.uk Xref: biosci bionet.software.staden:842 bionet.software:22776 Release 1999.0 -------------- We are pleased to announce that a new release of the package is now being prepared for shipping on CD. A summary of the changes and improvements is contained in: http://www.mrc-lmb.cam.ac.uk/pubseq/1999.0.html New Licensing method -------------------- Switching to CD (from previous release) has enabled us to do away with our requirement for all sites to sign and return a license agreement before we ship them the package. From Release 1999.0 onwards we will employ the common practice of making the license part of the packaging: if you break the seal you agree to the terms of the license. This will make it much easier for people to obtain the package, especially when coupled with the change described below. Package now completely FREE to academic users --------------------------------------------- Switching to CD has also cut our distribution costs, and by removing the need to handle the signed license agreements, we have reduced our administration load, so that we can now supply the whole package on CD FREE to academic users. This also means that we will no longer give the option for academic sites to pay in advance for all updates for the coming year: we will announce each release as it is ready for shipping and those who want it must email us with their request (and their address). Commercial users ---------------- There is no change to our prices for commercial sites but we will also change to the new licensing method and hence remove the need for signed agreements to be passed around. Windows NT version of the package --------------------------------- An alpha test version of the Windows NT port now exists. Please see the following web page for more details on this version. http://www.mrc-lmb.cam.ac.uk/pubseq/windows.html -- 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 Mon Feb 01 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.daimi.au.dk!not-for-mail From: Mikkel Holmen Andersen Newsgroups: bionet.software Subject: BioStat B Fermentor Software Date: Tue, 02 Feb 1999 19:07:55 +0100 Organization: Protein Chemistry Laboratory Lines: 35 Message-ID: <36B73EFB.52B5B02D@imsb.au.dk> Reply-To: mha@imsb.au.dk NNTP-Posting-Host: cmc.pchem.aau.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: xinwen.daimi.au.dk 917979040 22607 255.255.255.255 (2 Feb 1999 18:10:40 GMT) X-Complaints-To: news@daimi.au.dk NNTP-Posting-Date: 2 Feb 1999 18:10:40 GMT X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en Control and data collection software for the BioStat B fermentor. To collect process data and to control the fermentor an interface to PC running windows 95 has been made. All parameters can be controlled from the computer. With the software you can collect all process data which are displayed in a graphical window. Fermentation time and dates are logged as are user and remote connections. For further information and screen shots go to: http://imsb.au.dk/~mha/biohome.htm Regards, Mikkel H. Andersen ''~`` (\o-o/) +------------------------.oooO--(_)--Oooo.---------------------------+ | Protein Chemistry Laboratory | | Department of Molecular & Structural Biology, University of Aarhus | | Science Park, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark | | | | Tel.: +45 86 20 20 00 Fax: +45 86 13 65 97 ICQ: 160 419 57 | | | | mailto:mha@imsb.au.dk Home Page: http://imsb.au.dk/~mha/home.html | | .ooO | | ( ) Oooo. | +---------------------------\ (----( )-----------------------------+ \_) ) / (_/ +--------------------------------------------------------------------+ | Prions rule the inclusion body world | +--------------------------------------------------------------------+ From owner-software@net.bio.net Mon Feb 01 22:00:00 1999 Path: biosci!PUBLIC3.BTA.NET.CN!yszhao From: yszhao@PUBLIC3.BTA.NET.CN (Yinsuo Zhao) Newsgroups: bionet.software Subject: How to predict ribosome binding site in Bacteria using PC? Date: 2 Feb 1999 00:40:25 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <3.0.32.19990202163828.00692410@public3.bta.net.cn> NNTP-Posting-Host: net.bio.net To administrative of this group: I posted the following message on Jan 31. But it haven't appeared till now. So I have to post it again. Thank you for your help. ------------------------------------- Hi, Dear friends: I've cloned and sequenced a fragment from a kind of Gram-negative bacteria. I've analysed its ORF but I can't analysed the ribosome binding site in its promoter region. Does anyone know a free or shareware in PC (or any internet site) could do this work? Thanks for your good suggestion in advance. Best wishes, Yin-suo Zhao From owner-software@net.bio.net Mon Feb 01 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!dca1-hub1.news.digex.net!digex!newsfeed.cwix.com!166.93.8.12!natasha.rmii.com!news1.rmi.net!not-for-mail From: lisa_crawford@cmagroup.com Newsgroups: bionet.software Subject: Michigan; Director of Engineering; Medical Instrumentation, R&D, Hardware, Software Date: 2 Feb 1999 16:48:14 GMT Organization: Career Marketing Associates Lines: 46 Message-ID: <797a8e$s6h$1@news1.rmi.net> NNTP-Posting-Host: 206.247.5.216 X-Trace: news1.rmi.net 917974094 28881 206.247.5.216 (2 Feb 1999 16:48:14 GMT) X-Complaints-To: abuse@rmi.net NNTP-Posting-Date: 2 Feb 1999 16:48:14 GMT Southeast Michigan; Director of Engineering; Medical Instrumentation, R&D, Hardware, Software -Title: Director of Engineering -Location: SE Michigan -Full Time, Salaried, Excellent Benefits, Nice Bonus Plan (Solid Relocation Package) This professional will manage the R&D software and engineering groups. Responsible for the engineering design of new instrumentation systems which meet specification, quality, schedule and cost goals. Interface heavily with the instrument manufacturing and disposables development groups. Principal Duties and Responsibilities: Provide overall supervision of the R&D hardware and software engineering groups. Provide technical leadership as related to various internal and external issues. Responsible for the overall engineering design of new instrumentation systems. Assure that systems meet specifications and all quality, schedule and cost goals of development plans. Responsible for the manufacturability of all designs. Interface heavily with the instrument and disposables manufacturing groups. Manage the hiring and maintenance of engineering resources required to support product development program. Maintain an awareness of new technologies and identify those which might be applied to help achieve the short and long term goals. Minimum Skill and Knowledge Requirements or Equivalent Masters degree in engineering. Ten years of project management and R&D departmental management experience. Ability to analyze complex information relating to a broad spectrum of technical, market and general business situations. Must be knowledgeable of medical instrumentation, specifically clinical laboratory and patient monitoring applications. Please refer to JO# 7742RJS in your response. lisa_crawford@cmagroup.com Lisa Crawford Sr. Researcher & Associate Recruiter ljc@cmagroup.com IT & Software Solutions Team Career Marketing Associates http://www.cmagroup.com/IT.html From owner-software@net.bio.net Mon Feb 01 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!166.93.8.12!natasha.rmii.com!news1.rmi.net!not-for-mail From: lisa_crawford@cmagroup.com Newsgroups: bionet.software Subject: Florida; Staff Scientist/Engineer; Electrophysiology, Algorithms, Signal Processing Date: 2 Feb 1999 16:42:20 GMT Organization: Career Marketing Associates Lines: 31 Message-ID: <7979tc$s2j$1@news1.rmi.net> NNTP-Posting-Host: 206.247.5.216 X-Trace: news1.rmi.net 917973740 28755 206.247.5.216 (2 Feb 1999 16:42:20 GMT) X-Complaints-To: abuse@rmi.net NNTP-Posting-Date: 2 Feb 1999 16:42:20 GMT Florida; Staff Scientist/Engineer; Electrophysiology, Algorithms, Signal Processing -Title: Staff Scientist/Engineer -Location: Florida -Salaried, Full-Time, Excellent Benefits (Excellent Relocation Package Available) This professional will be actively involved in leading advanced cardiovascular EP product development. Ideal candidate will have PhD/MS in either Biomedical Engineering, CS, EE, Physics or Computer Science with a solid clinical appreciation of cardiovascular electrophysiology. Technical skills should include: Advanced algorithms, signal processing and software development. Experience with Windows NT, Win32 and C/C++ skills would be a plus. Must bring in EP expertise either through engineering, or through the science route; preferably both. Ideal candidate will have industrial, or have collaborated in an industrial product development effort. Technical leadership/mentoring experience would also be helpful. Please refer to JO# 7216RJS in your response. lisa_crawford@cmagroup.com Lisa Crawford Sr. Researcher & Associate Recruiter ljc@cmagroup.com IT & Software Solutions Team Career Marketing Associates http://www.cmagroup.com/IT.html From owner-software@net.bio.net Mon Feb 01 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!166.93.8.12!natasha.rmii.com!news1.rmi.net!not-for-mail From: lisa_crawford@cmagroup.com Newsgroups: bionet.software Subject: Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging Date: 2 Feb 1999 16:27:19 GMT Organization: Career Marketing Associates Lines: 27 Message-ID: <797917$rfc$1@news1.rmi.net> NNTP-Posting-Host: 206.247.5.216 X-Trace: news1.rmi.net 917972839 28140 206.247.5.216 (2 Feb 1999 16:27:19 GMT) X-Complaints-To: abuse@rmi.net NNTP-Posting-Date: 2 Feb 1999 16:27:19 GMT West Palm, Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging **We are also working similar medical imaging software positions for clients in NE USA, Midwest, PNW, CA and BC Canada. -Senior Software Engineer -Southeast Florida Coastal -Salaried, Full-Time, Excellent Benefits (Relocation Assistance Available) Medical DICOM knowledge would be a major plus. Experience with C/C++ and NT required. Image manipulation, compression, edge detection, analysis, all good things to have. Please refer to JO# 5253RJS in your response. lisa_crawford@cmagroup.com Lisa Crawford Sr. Researcher & Associate Recruiter ljc@cmagroup.com IT & Software Solutions Team Career Marketing Associates http://www.cmagroup.com/IT.html From owner-software@net.bio.net Mon Feb 01 22:00:00 1999 From: "GhEtTo BoY" Newsgroups: bionet.software Subject: You can download software,freeware and shareware at: Date: Tue, 2 Feb 1999 15:06:55 -0800 Lines: 4 X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 NNTP-Posting-Host: pm2-70.connection.com Message-ID: <36b75791.0@204.138.111.13> X-Trace: 2 Feb 1999 14:52:49 +0500, pm2-70.connection.com Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!logbridge.uoregon.edu!router1.news.adelphia.net!cyclone.news.idirect.com!island.idirect.com!news1.tor.metronet.ca!204.138.111.13!pm2-70.connection.com http://www.freewareworld.com From owner-software@net.bio.net Mon Feb 01 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news-peer1.sprintlink.net!-program!news-backup-west.sprintlink.net!news.sprintlink.net!newsfeed.embratel.net.br!news.zaz.com.br!not-for-mail From: "ZAZ - News" Newsgroups: bionet.software Subject: Analise de crescimento de plantas Date: Tue, 2 Feb 1999 14:53:29 -0200 Organization: ZAZ/NutecNet Lines: 4 Message-ID: <797apc$mqf$1@srv4-poa.nutecnet.com.br> NNTP-Posting-Host: 200.210.222.189 X-Trace: srv4-poa.nutecnet.com.br 917974636 23375 200.210.222.189 (2 Feb 1999 16:57:16 GMT) X-Complaints-To: abuse@zaz.com.br NNTP-Posting-Date: 2 Feb 1999 16:57:16 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Atravez da analise de crescimento de plantas, é possivel escrever software s que simulam o seu desenvolvimento. From owner-software@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news-feed.ifi.uio.no!uninett.no!news.net.uni-c.dk!not-for-mail From: Flemming Larsen Newsgroups: bionet.software Subject: Prediction of solubility of recombinant proteins in E.coli. Date: Wed, 03 Feb 1999 12:30:54 +0100 Organization: UNI-C Lines: 18 Message-ID: <36B8336D.DD2634FA@remove-this.biobase.dk> NNTP-Posting-Host: 130.226.107.84 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.net.uni-c.dk 918041406 28246 (None) 130.226.107.84 X-Complaints-To: usenet@news.net.uni-c.dk X-Mailer: Mozilla 4.04 [en] (Win95; I) Hi, Has anybody ever seen a program that calculates the solubility of recombinant proteins expressed in E.coli. solely based on the amino acid composition of a protein? Please e-mail your reply to flar@biobase.dk since I do not follow this newsgroup regularly. Regards, Flemming National University Hospital Dept. Clin. Immunol. Copenhagen Denmark From owner-software@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!news.icnet!not-for-mail From: islam Newsgroups: bionet.software Subject: Re: minimal sphere Date: Wed, 03 Feb 1999 11:43:09 +0000 Organization: Imperial Cancer Research Fund Lines: 32 Message-ID: <36B8364D.41C6@icrf.icnet.uk> References: <7972t5$59lq@moka.ccr.jussieu.fr> NNTP-Posting-Host: palm.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX 6.3 IP32) Out of curiosity, what do you mean by a minimal sphere ? E.g. Smallest (Volume) sphere to enclose all atoms, Least Squares fitted sphere ... Michel PETITJEAN wrote: > > Subj: minimal sphere > > A colleague told me recently that it should be useful to have a > programme computing the minimal sphere containing a molecule, > together with various shape coefficients. > I have done it. > Binaries are available for DEC-alpha (VMS and unix), RS6000 serie > (and SP2) CRAY Y and J90, SGI O2 (and various mips1 to mips4). > Interested people should email me, without forgetting to tell which > computer is used. > > Michel Petitjean, Email: petitjean@itodys.jussieu.fr > ITODYS (CNRS, ESA 7086) ptitjean@ccr.jussieu.fr > 1 rue Guy de la Brosse Phone: +33 01 44 27 48 57 > 75005 Paris, France. FAX : +33 01 45 84 98 25 ____________________________________________ Suhail A Islam Biomolecular Modelling Laboratory Imperial Cancer Research Fund, P.O. Box 123 44 Lincoln's Inn Fields, London WC2A 3PX Tel: (0171) 269 3380 Fax: (0171) 269 3258 email: islam@icrf.icnet.uk http://www.icnet.uk/bmm/ ____________________________________________ From owner-software@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.wli.net!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed1.swip.net!swipnet!newsfeed1.uni2.dk!news.net.uni-c.dk!not-for-mail From: Flemming Larsen Newsgroups: bionet.software Subject: Prediction of solubility of recombinant proteins in E.coli. Date: Wed, 03 Feb 1999 12:12:16 +0100 Organization: UNI-C Lines: 18 Message-ID: <36B82F0E.662084E0@remove-this.biobase.dk> NNTP-Posting-Host: 130.226.107.243 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.net.uni-c.dk 918040271 30274 (None) 130.226.107.243 X-Complaints-To: usenet@news.net.uni-c.dk X-Mailer: Mozilla 4.04 [en] (Win95; I) Hi, Has anybody ever seen a program that calculates the solubility of recombinant proteins expressed in E.coli. solely based on the amino acid composition of a protein? Please e-mail your reply to flar@biobase.dk since I do not follow this newsgroup regularly. Regards, Flemming National University Hospital Dept. Clin. Immunol. Copenhagen Denmark From owner-software@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newspeer.monmouth.com!oleane!jussieu.fr!saphir.jouy.inra.fr!tuinen From: tuinen@epoisses.inra.fr (Diederik van Tuinen) Newsgroups: bionet.software Subject: aligned sequences editing software Followup-To: bionet.molbio.methds-reagnts Date: Wed, 03 Feb 1999 16:56:31 +0100 Organization: LPA INRA/CMSE Lines: 11 Message-ID: NNTP-Posting-Host: mac2.epoisses.inra.fr Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 I am looking for a software, hopefully shareware and runing on MacOS, allowing to edit aligned sequences - adding or removing gaps - after a clustalv run. -- Dr. D. van Tuinen INRA Laboratoire de Phytoparasitologie INRA/CNRS Centre de Microbiologie du Sol et de l'Environnement Domaine d'Epoisses 21110 BRETENIERES From owner-software@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!nntp.flash.net!newspeer.monmouth.com!oleane!jussieu.fr!saphir.jouy.inra.fr!tuinen From: tuinen@epoisses.inra.fr (Diederik van Tuinen) Newsgroups: bionet.software Subject: aligned sequences editing software Date: Wed, 03 Feb 1999 16:54:29 +0100 Organization: LPA INRA/CMSE Lines: 11 Message-ID: NNTP-Posting-Host: mac2.epoisses.inra.fr Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 I am looking for a software, hopefully shareware and runing on MacOS, allowing to edit aligned sequences - adding or removing gaps - after a clustalv run. -- Dr. D. van Tuinen INRA Laboratoire de Phytoparasitologie INRA/CNRS Centre de Microbiologie du Sol et de l'Environnement Domaine d'Epoisses 21110 BRETENIERES From owner-software@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.xcom.net!newspeer.monmouth.com!oleane!jussieu.fr!saphir.jouy.inra.fr!tuinen From: tuinen@epoisses.inra.fr (Diederik van Tuinen) Newsgroups: bionet.software Subject: aligned sequences editing software Followup-To: bionet.molbio.methds-reagnts Date: Wed, 03 Feb 1999 16:55:48 +0100 Organization: LPA INRA/CMSE Lines: 11 Message-ID: NNTP-Posting-Host: mac2.epoisses.inra.fr Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 I am looking for a software, hopefully shareware and runing on MacOS, allowing to edit aligned sequences - adding or removing gaps - after a clustalv run. -- Dr. D. van Tuinen INRA Laboratoire de Phytoparasitologie INRA/CNRS Centre de Microbiologie du Sol et de l'Environnement Domaine d'Epoisses 21110 BRETENIERES From owner-software@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!feed1.news.rcn.net!rcn!cpk-news-hub1.bbnplanet.com!news.gtei.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!ics1a.sanger.ac.uk!birney From: Ewan Birney Newsgroups: bionet.software Subject: Pfam Release 3.4 Date: Wed, 3 Feb 1999 10:16:27 +0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 49 Message-ID: NNTP-Posting-Host: ics1a.sanger.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 918036989 16074 193.60.84.184 (3 Feb 1999 10:16:29 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 3 Feb 1999 10:16:29 GMT ANNOUNCING PFAM RELEASE 3.4 =========================== Pfam is a collection of protein domain family alignments which were constructed semi-automatically using profile hidden Markov models. Pfam families contain functional annotation and cross-references to other databases. Query sequences can be searched against the Pfam library of profile hidden Markov models at the web sites below. Pfam 3.4 contains 1407 families. 57% of proteins in SWISSPROT 35 and TrEMBL 5 have at least one match to a Pfam family. The changes between Pfam release 3.4 and Pfam release 3.3 are discussed below. 18 new families have been added including the collagen triple helical repeat, which is found in 390 proteins. The zn-protease familiy has been removed because it only covered the active site of a large superfamily and was not able to discriminate well between members and non-members of the family. The zn-protease family is being replaced by a number of subfamilies. For interactive access and searching see URLs http://www.sanger.ac.uk/Software/Pfam/ http://pfam.wustl.edu/ http://kisac.cgr.ki.se/Pfam/ The release is also available in flat file by anonymous ftp: ftp://ftp.sanger.ac.uk/pub/databases/Pfam/ ftp://ftp.genetics.wustl.edu/pub/Pfam/ The Pfam HMM library is compatible with HMMER2 software, available from http://hmmer.wustl.edu/ ___________________ The Pfam consortium 99-01 Ewan Birney http://www.sanger.ac.uk/Users/birney/ From owner-software@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.cwix.com!193.174.75.110!news-was.dfn.de!news-fra1.dfn.de!news.uni-mainz.de!not-for-mail From: "Dr. Klaus Eimert" Newsgroups: bionet.software Subject: time laps with frame grabber card ? Date: Wed, 03 Feb 1999 15:27:02 +0100 Organization: Dept. of Botany, Geisenheim Research Institute Lines: 30 Message-ID: <36B85CB6.27C82418@geisenheim.fa.fh-wiesbaden.de> Reply-To: eimert@geisenheim.fa.fh-wiesbaden.de NNTP-Posting-Host: ascend.mnd.fh-wiesbaden.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en,zh,zh-CN,zh-TW,de Dear netters, maybe somebody could help me solving a technical(?) problem. I have a video camera connected to a PC with a frame grabber card. Pictures are taken via a TWAIN interface. Although it's a Win95 system I have to use 16 bit software for capture. Now the question - is there any software (16 bit, preferrably free or shareware) which allows me to take a picture automatically, say every 15 or 30 minutes for a time course of 3-4 days? It is just a matter of finance - I know that there is some video equipment which allows to do just that. But since we have a VERY tight budget buying new equipment is not an option. Any ideas? Any suggestion is greatly appreciated!!! Sincerely, Klaus -- ---------------------------------------------------------------- Dr. Klaus Eimert Dept. of Botany The State Research Institute Geisenheim Von-Lade-Str. 1 D-65366 Geisenheim Germany Phone: + 49 6722 502 469 FAX : + 49 6722 502 460 E-mail: eimert@geisenheim.fa.fh-wiesbaden.de URL: http://www.mnd.fh-wiesbaden.de/fag/bio/bo/ebostart.html ---------------------------------------------------------------- From owner-software@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!oleane!jussieu.fr!moka.ccr.jussieu.fr!not-for-mail From: ptitjean@ccr.jussieu.fr (Michel PETITJEAN) Newsgroups: bionet.software Subject: Re: minimal sphere Date: 3 Feb 1999 14:25:01 +0100 Organization: CCR - Universites Paris VI/VII - Paris - France Lines: 12 Message-ID: <799ind$2vmi@moka.ccr.jussieu.fr> NNTP-Posting-Host: moka.ccr.jussieu.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit References: <7972t5$59lq@moka.ccr.jussieu.fr> <36B8364D.41C6@icrf.icnet.uk> islam wrote: >Out of curiosity, what do you mean by a minimal sphere ? >E.g. Smallest (Volume) sphere to enclose all atoms, Least Squares >fitted sphere ... The smallest (volume) sphere enclosing the atomic centers. Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, ESA 7086) ptitjean@ccr.jussieu.fr From owner-software@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!dca1-hub1.news.digex.net!digex!diablo.theplanet.net!dispose.news.demon.net!demon!nntp.news.xara.net!xara.net!server6.netnews.ja.net!server4.netnews.ja.net!server2.netnews.ja.net!pegasus.csx.cam.ac.uk!mole.bio.cam.ac.uk!csg From: Caroline Gerrard Newsgroups: bionet.software Subject: Restriction fragment mapping programs Date: Wed, 3 Feb 1999 15:14:12 +0000 Organization: University of Cambridge, England Message-ID: NNTP-Posting-Host: mole.bio.cam.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Lines: 18 Hi I'm new to this group, so apologies if this old stuff. I'm trying to find a program which will allow me input data from restriction digests, subsequently blotted and probed with known markers, and create a map of the digest pattern. The program has to be either Mac or PC. There are loads of things for sequence alignment, but this is on bigger scale and there's no sequence available. The only thing I've found so far is 'Double Digester' which isn't really suitable and causes our rather old Mac to crash. Any help/advice? Thanks Caro From owner-software@net.bio.net Wed Feb 03 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.wli.net!sunqbc.risq.qc.ca!torn!newshost.uwo.ca!marvin.biochem.uwo.ca!user From: ggloor@julian.uwo.ca (Greg) Newsgroups: bionet.software Subject: Re: DNA sequence analysis for Mac Date: Thu, 04 Feb 1999 09:31:45 -0500 Organization: U.W.O. Lines: 14 Message-ID: References: <36B31D13.7366F38E@icr.ac.uk> NNTP-Posting-Host: marvin.biochem.uwo.ca In article <36B31D13.7366F38E@icr.ac.uk>, paraic@icr.ac.uk wrote: DNA Strider does all the basic DNA manipulations. It is cheap (US$200 and very fast. email Christian Marck marck@jonas.saclay.cea.fr > paraic@icr.ac.uk -- Best Regards.....Greg Gloor | You cannot exploit what you have not | ggloor@julian.uwo.ca | discovered. | 519-661-3526 fax 519-661-3175 | Basic Science is important! | http://www.biochem.uwo.ca/ |------------ My thoughts -------------| From owner-software@net.bio.net Wed Feb 03 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!diablo.theplanet.net!dispose.news.demon.net!demon!nntp.news.xara.net!xara.net!server6.netnews.ja.net!st-and!etd From: etd@bigfoot.com (Edwin ten Dam) Newsgroups: bionet.software Subject: Re: aligned sequences editing software Date: Thu, 04 Feb 1999 13:04:03 +0000 Organization: School of Biomedical Sciences - University of St Andrews Message-ID: References: NNTP-Posting-Host: bmsmac-mdr1.st-and.ac.uk X-Newsreader: MT-NewsWatcher 2.4.4 X-Face: -P+89ASh_wrs;AUGm`!l[}/o-lyK}5W.gq\fkJ{#d6Gu,hWrZNz::iMm5PJb} __A96]-LUrl)X=uF=V|\3-\9/sXvBs/H Lines: 33 In article , tuinen@epoisses.inra.fr (Diederik van Tuinen) wrote: >I am looking for a software, hopefully shareware and runing on MacOS, >allowing to edit aligned sequences - adding or removing gaps - after a >clustalv run. You might want to give Andrew Rambaut's multiple alignment editor "Se-Al" a try. This is a Mac only program for compiling, manipulating and editing multiple sequence alignments. It currently features on the fly translation of protein-coding DNA (so that you can edit the amino-acid alignment and the underlying nucleotides will be aligned accordingly). You can drag regions and copy and paste. Searching for motifs is a bit primative. It's under development at the moment. Alternatively, ClustalX has some minor editing features: ftp://ftp.ebi.ac.uk//pub/software/mac/clustalw/clustalx/clustalx1.64b.PPC.sea.Hqx and is worth a look anyway for its GUI on top of ClustalW. Seqpup/SeqApp was already mentioned, so I won't go into that. cheers, Edwin -- Edwin ten Dam etd@bigfoot.com School of Biomedical Sciences - University of St Andrews Biomolecular Sciences Bldng, North Haugh, St Andrews, KY16 9ST U.K. Phone: +44 1334 463404 - Fax: +44 1334 462595 From owner-software@net.bio.net Wed Feb 03 22:00:00 1999 Path: biosci!CGIAR.ORG!L.SHEN From: L.SHEN@CGIAR.ORG (Shen Lishuang) Newsgroups: bionet.software Subject: Graphic Output for Genetic Linkage Map, Graphical Genotypes and QTL Plot on PCs Date: 4 Feb 1999 06:11:31 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 88 Sender: daemon@net.bio.net Distribution: world Message-ID: <004501be5048$a9822a60$8ce65dc6@pbgb-up3.irri.cgiar.org> Reply-To: Shen Lishuang NNTP-Posting-Host: net.bio.net To all: I have just written a program, Mapplotter, which can be used to get graphic output on PC computer. Mapplotter is primarily designed to plot Genetic Linkage Map, Graphical Genotypes and draw QTL plot according to results from other programs. It also bear a picture viewer module for browsing different formats of image files and a Rich Text Editor module for viewing and modifying data and result files.. Mapplotter Version 1.1 has the below functions: 1. Drawing genetic maps, graphical genotypes and QTL plots, drawn maps are saved as 256-color bitmap files. 2. It lets you specify the scale on both X-axis and Y-axis. Marker names are printed in their exact position on map. 3. For graphical genotypes, it works for DH, RIL, BC and F2 populations at present. Regions from different parents are show in different colors and fillstyles. It also give genome ratio of each plant in "genome ratio.txt" file. 4. Drawing multiple plants (for graphical genotypes ) or traits (for QTL plots) in one run. 5. For QTL plots, it can draw a single trait a time or up to 3 traits a time. You can choose to draw QTL analysis mode of SIM, CIM or both on one plot. It also enables you choose to show the sign of additive effects on QTL plots. 6. For QTL plot, three QTL result formats are supported now. Two of them are the same as in QTLCartographer (Zmapqtl.exe result files and Preplot.exe result files) from North Carolina State University. Other format can also be added on request. It lets you choose using LOD score or liklihood ratio (LR) for your own QTL result file and centiMorgan (cM) or Morgan (M) for your map data file. 7. For genetic map data , two formats are supported. One is the same as in QTLCartographer, the other format can be easily modified from Mapmaker/EXP output file. 8. Built-in image viewer enables you quickly browse through your maps. It can view bitmap, metafile and icon files. It also enables you do simple editing of the drawn maps. 9. Built-in image viewer can display the map position and LOD score of any point in your QTL plots by simply clicking and moving mouse on the drawn maps. 10. Most commands are self-evident. Besides, you can also get hints for some of them by placing mouse cursor on them. Mapplotter is a Windows 95 program and is freely available for acedemic use. More functions will be added in future. Please give it a try and test it. For QTL plotting, more data format for QTL results can be added upon request. For details and how to getting the program, please contact with the author. Best regards, Lishuang Shen Project Scientist Plant Breeding, Genetics and Biochemistry Division International Rice Research Institute (IRRI) P.O. Box 3127 Makati Central Post Office (MCPO) 1271 Makati City Philippines Tel: (63-49)5360672 (home) or (63-2) 8450563-local 540 (Office) Fax: (63-2)-8450606 or (63-2)-8450563 Email: lshen@irri.cgiar.org From owner-software@net.bio.net Wed Feb 03 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!oleane!jussieu.fr!saphir.jouy.inra.fr!lindenb From: lindenb@jouy.inra.fr (Pierre Lindenbaum) Newsgroups: bionet.software Subject: Re: Restriction fragment mapping programs Date: 4 Feb 1999 08:37:47 GMT Organization: INRA Lines: 22 Message-ID: <79bm8r$b26$1@saphir.jouy.inra.fr> References: NNTP-Posting-Host: biotec.jouy.inra.fr X-Newsreader: TIN [version 1.2 PL2] In article you wro$ : Hi : I'm new to this group, so apologies if this old stuff. I'm trying to find : a program which will allow me input data from restriction digests, : subsequently blotted and probed with known markers, and create a map of : the digest pattern. The program has to be either Mac or PC. On the WWW you could try CloneIt CloneIt ONLINE http://topaze.jouy.inra.fr/cgi-bin/CloneIt/CloneIt or try the text-based version CloneIt WWW Home Page http://locus.jouy.inra.fr/soft/cloneit/cloneit.html Hope it helps. Pierre LINDENBAUM From owner-software@net.bio.net Wed Feb 03 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsgate.cuhk.edu.hk!news.hku.hk!hkusub.hku.hk!not-for-mail From: Xia Xuhua Newsgroups: bionet.software Subject: DAMBE Software package Date: 4 Feb 1999 01:53:45 GMT Organization: The University of Hong Kong Lines: 85 Message-ID: <79auj9$df15@hkusud.hku.hk> NNTP-Posting-Host: 147.8.145.42 X-Newsreader: TIN [UNIX 1.3 release 961025] Dear All, DAMBE (for data analysis in molecular biology and evolution) is available at http://web.hku.hk/~xxia/software Here is a list of DAMBE features: ---File input with commonly used DNA and protein sequence formats, including MEGA (interleaved and sequential), Pearson/FASTA, ClustalW, IG (IntelliGenetics), GB (GenBank), GCG single-sequence (.GCG) and multi-sequence format(.MSF), Yang's PAML format (interleaved and sequential, but not the one with the G option) and RST format, Kumar's PHYLTEST format, as well as those formats understood by Don Gilbert's READSEQ (which is included for your convenience). One particular strength of the program lies in its versatility with the GenBank (GB) file format - the program can automatically splice out and join CDS, exons, introns, mRNA segments according to the FEATURES table in the GB file. ---File conversion between commonly used sequence formats. ---Saving subsets of sequences in any of commonly used format. ---Many convenient ways of manipulating nucleotide and amino acid sequences. ---Many descriptive statistics of molecular sequences. ---Generating distance matrices including Jukes and Cantor's (1969) distance, Kimura's (1980) two-parameter distance, Tajima and Nei's (1984) distance, Lake's (1994) paralinear distance, and an entropy-based distance which seems to perform better in phylogenetic reconstruction than other distances based on preliminary studies. ---Phylogenetic analyses using distance, maximum parsimony and maximum likelihood methods; resampling statistics (bootstrap and jackknife). ---Graphically display phylogenetic trees (including consensus tree) and topology manipulation. ---For pair-wise differences, one particular strength of the program lies in its ability to count the differences between neighboring nodes along a phylogenetic tree if the tree structure is provided. For example, the BASEML program in the PAML package can reconstruct ancestral sequences when a topology is given. The output file from BASEML, called rst by default, contains the tree topology as well as the reconstructed sequences. DAMBE can read the RST file directly and count pair-wise differences in nucleotide, amino acid and codon sequences between neighboring nodes along the phylogenetic tree. ---Fit the Poisson and negative binomial distributions to nucleotide, amino acid, and codon substitutions along the DNA sequences. ---Computing expected pattern of codon substitution given a genetic code (e.g., mammalian mitochondrial), with or without adjustment for codon frequencies. All 12 different genetic codes have been implemented. ---Quantifying the extent of substitution saturation in nucleotide sequences for one to decide whether to include or exclude certain nucleotide sites in phylogenetic reconstruction ---Plotting amino acid properties (chemical composition along the side chain, volume, polarity, polar requirement, hydropathy, aromaticity, and isoelectric point) along sequences ---Computing an entropy-based measure of variability over sites and plot the variability along the sequences. ---Special computational tools for analyzing the effect of DNA methylation on molecular evolution of nucleotide sequences. The strength of DAMBE is not in what it can do, but in the way it does it, which I believe will save many researchers many hours. Best. Xuhua =================================================================== Xuhua Xia | Tel: (852) 2857 8239 (lab) Assistant Professor | Tel: (852) 2975 5629 (office) Department of Ecology & Biodiversity| Fax: (852) 2517 6082 The University of Hong Kong | Email: xxia@hkusua.hku.hk Pukfulam Road | WWW: http://web.hku.hk/~xxia Hong Kong | =================================================================== From owner-software@net.bio.net Wed Feb 03 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!diablo.theplanet.net!dispose.news.demon.net!demon!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Hans Sluiman Newsgroups: bionet.software Subject: Re: aligned sequences editing software Date: Thu, 04 Feb 1999 12:35:40 +0000 Organization: MRC Human Genome Mapping Project Resource Centre Sender: hsluiman@pc103.rbge.org.uk Message-ID: <36B9941A.1655A7B@rbge.org.uk> References: NNTP-Posting-Host: pc103.rbge.org.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 918131585 16836 193.62.154.134 (4 Feb 1999 12:33:05 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 4 Feb 1999 12:33:05 GMT To: Diederik van Tuinen X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) X-Accept-Language: en Lines: 59 Diederik van Tuinen wrote: > > I am looking for a software, hopefully shareware and runing on MacOS, > allowing to edit aligned sequences - adding or removing gaps - after a > clustalv run. > > -- > Dr. D. van Tuinen > INRA > Laboratoire de Phytoparasitologie INRA/CNRS > Centre de Microbiologie du Sol et de l'Environnement > Domaine d'Epoisses > 21110 BRETENIERES SeqPup, version 0.7, August 1997 see the folder iubio:/molbio/seqpup/java/ for this new version see the folder iubio:/molbio/seqpup/c++/ for the older, but currently more complete version SeqPup is a biological sequence editor and analysis program. It includes links to network services and external analysis programs. It is usable on common computer systems, including Macintosh, MS-Windows and X-Windows. Features include multiple sequence alignment and single sequence editing ! read and write several sequence file formats *! sequence feature editing, and marking in prints translate dna/amino, consensus, reverse/complement, distance and such functions pretty print of alignments and sequences with boxed and shaded regions Internet sequence analysis: * fetch sequeces using SRS keyword search * NCBI-BLAST similarity search (this version: * - new; ! - incomplete) NOTICE: This application is a work in progress; it has bugs. It may be useful to you as is, but it is still prone to problems. Find this software at ftp://iubio.bio.indiana.edu/molbio/seqpup/ http://iubio.bio.indiana.edu/soft/molbio/seqpup/ SeqPup is being written using DCLAP, a free and portable class application framework, now converted to the new Java language. This Java version will work on any computer system that supports Java runtime version 1.0.2, including Macintosh, MS Windows, and many Unix systems. Java versions of other molecular biology applications of mine will soon be updated (maybe by 26 Aug 97): loopDloop - an RNA secondary structure display editor Phylodendron - a phylogenetic tree drawing application FlyNapp - a FlyBase database network application Developers will find the source code for this application and others in the iubio:/molbio/java/source folders. From owner-software@net.bio.net Wed Feb 03 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!xfer.kren.ne.kr!h5nntp1.channeli.net!b5nntp2.channeli.net!not-for-mail From: Senovia von Perle Newsgroups: bionet.software Subject: [Wanted] Biotechnology related SW Date: Fri, 05 Feb 1999 06:56:26 +0900 Organization: IMBG Lines: 25 Sender: senovia@210.112.181.91 Message-ID: <36BA1785.CD046B47@chollian.net> NNTP-Posting-Host: 210.112.181.91 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Trace: b5nntp2.channeli.net 918165400 18658 210.112.181.91 (4 Feb 1999 21:56:40 GMT) X-Complaints-To: usenet@b5nntp2.channeli.net NNTP-Posting-Date: 4 Feb 1999 21:56:40 GMT X-Mailer: Mozilla 4.07 (Macintosh; I; PPC) Hi, there! I want to list biotechnology related software in my web page. Molecular biology, Genetics, Biochemistry... etc. Every topic is permitted. Commercial, non-commercial is not critical. He/She who wants to propagate his/her own s/w may take this chance... Commercial s/w company, too. I want to you to help me. Reply form is : 1) SW name 2) SW provider (individual/company) 3) SW location (Web site) 4) SW Commercial/shareware/freeware 5) Platform (Mac favoured/Win/Unix) I expect your help. Best Regards Senovia von Perle email : senovia@chollian.net From owner-software@net.bio.net Wed Feb 03 22:00:00 1999 Path: biosci!student.ul.ie!9513574 From: 9513574@student.ul.ie (DAFFY SINEAD CLAIR) Newsgroups: bionet.software Subject: re:restriction fragment mapping programs Date: 4 Feb 1999 07:00:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <36EAF78F3E72D21190B500A0C9612D9580FE30@gabriel.ul.ie> NNTP-Posting-Host: net.bio.net Hi Glad to see that somone (i.e. Caroline) is experiencing the same difficulties as myself! I am also trying to locate a program (or programs) for the analysis of double digest restriction patterns, with a view to obtaining a linear of preferably a circular restriction map. However, it cannot be Mac based as my university does not possess such a computer system, hence I am interested in Windows based programs. Any help on this matter would be greatly appreciated. This area forms the basis of my final year thesis and at this stage I am desperate. Thanks, Sinead From owner-software@net.bio.net Wed Feb 03 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!feed1.news.rcn.net!rcn!newsfeed.cwix.com!152.163.199.19!portc03.blue.aol.com!audrey01.news.aol.com!not-for-mail From: haroldb786@aol.com (HaroldB786) Newsgroups: bionet.software Subject: re:restriction fragment mapping programs Lines: 11 NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Date: 4 Feb 1999 16:59:02 GMT Organization: AOL http://www.aol.com References: <36EAF78F3E72D21190B500A0C9612D9580FE30@gabriel.ul.ie> Message-ID: <19990204115902.26738.00000620@ng-fq1.aol.com> You might try the program Karl has been working on- ftp://ftp.netcom.com/pub/ka/karl/GEL.EXE. Depending on what format your sequences are in.... txt, fasta, (?) this program will do single, double or multiple digestions.... There are "plasmid" digestion programs out there.... check EBI (http://www.EBI.ac.uk) software section.... If this is not enough, email me... harold berninghausen From owner-software@net.bio.net Wed Feb 03 22:00:00 1999 Path: biosci!YAHOO.COM!dureti2 From: dureti2@YAHOO.COM Newsgroups: bionet.software Subject: (none) Date: 4 Feb 1999 11:46:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 69 Sender: daemon@net.bio.net Distribution: world Message-ID: <199902041945.LAA27894@net.bio.net> NNTP-Posting-Host: net.bio.net We'll Submit Your Site To Over 900 Search Engines, Directories, & Indices For A "One Time Cost" Of Only $ 39.95 *** 100% Money Back Guarantee *** *** Immediately Increase Your Sites Exposure *** For Less Than 4 Cents Each We Will Submit Your Web Site To Over 900 Of The Net's Hottest Search Engines, Directories & Indices. If your site isn't listed in the Search Engines, how can people find you to buy your products or services? 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Call us toll free at (800) 771-2003 in the USA and Canada or outside the USA at (916) 771-4739 and we'll provide you with all the necessary information to get you submitted Right Away. #2488 To be removed from our mailing list, please respond with the word remove in the subject. From owner-software@net.bio.net Thu Feb 04 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news-peer1.sprintlink.net!-program!news-in-east1.sprintlink.net!news.sprintlink.net!itssrv1.ucsf.edu!macmac-2.ucsf.edu!user From: bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD) Newsgroups: bionet.software Subject: Re: 16 Bit Gel Doc anyone? Date: Thu, 04 Feb 1999 21:29:40 -0700 Organization: University of California, San Francisco Lines: 14 Message-ID: References: <36b0e70f.0@rboc1.prime-x.net> NNTP-Posting-Host: macmac-2.ucsf.edu In article <36b0e70f.0@rboc1.prime-x.net>, "Sean" wrote: > Comparison Table Was is just my newsreader or was the "table" just a random mess of text, numbers and prices? Sorry Sean, your company must be a real cowboy outfit if you spam so many newsgroups with meaningless drivel. Bernard -- Bernard P. Murray, PhD Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA From owner-software@net.bio.net Thu Feb 04 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.wli.net!news-xfer.newsread.com!netaxs.com!newsread.com!news.hardlink.com!stalker.oem.net!not-for-mail From: "Sean" Newsgroups: bionet.software Subject: 16 Bit Gel Doc anyone? Date: Fri, 29 Jan 1999 04:43:09 -0500 Organization: oemnetworks.com Lines: 29 Message-ID: <36b0e70f.0@rboc1.prime-x.net> NNTP-Posting-Host: rboc1.prime-x.net X-Trace: stalker.oem.net 918155280 10682 209.113.154.11 (4 Feb 1999 19:08:00 GMT) X-Complaints-To: usenet@stalker.oem.net NNTP-Posting-Date: 4 Feb 1999 19:08:00 GMT X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Comparison Table of Gel Doc , Chemiluminescence & Microscopy with Cooled integrating 16-bits Monochrome & 24-bits color. Biostorm Cooled Integrating CCD video Camera 16-bits 8-bits Resolution, Gray levels 65,356 256 Max. integration time , Gel Documentation with UV transilluminator, (background cause bleaching) 40 seconds 3 seconds Max Integration time, Chemiluminescence, No UV Transilluminator. (Dark current cause bleaching), 90 minutes 5 minutes Upgrade for any system:CCD, grabber, on-chip software $5,365(16-bits) $5,950(8-bits) Chemi-16 system, complete system $16,995 Over $18,950 24-bits color cooled CCD with grabber interface $5,895 $5,950 (not cooled) From owner-software@net.bio.net Thu Feb 04 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.cwix.com!207.110.0.61!news.connectnet.com!not-for-mail From: "Philip Miller" Subject: Bioinformatics workshop Newsgroups: bionet.software Message-ID: <01be5529$747e31c0$4d6513ce@funtv.com> X-Newsreader: Microsoft Internet News 4.70.1161 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_01BE54E6.665AF1C0" Content-Transfer-Encoding: 7bit Lines: 26 Date: Fri, 05 Feb 1999 19:24:19 GMT NNTP-Posting-Host: 206.19.101.77 X-Trace: news.connectnet.com 918242659 206.19.101.77 (Fri, 05 Feb 1999 11:24:19 PDT) NNTP-Posting-Date: Fri, 05 Feb 1999 11:24:19 PDT This is a multi-part message in MIME format. ------=_NextPart_000_01BE54E6.665AF1C0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit The workshop, Advanced Bioinformatics, taught at UCSD, has a webpage with course outline, references, links and exercises at: www.bioinfotech.com/AdvancedBioinformatics.html Philip Miller, PhD BITS: Bioinformational Technical Services ------=_NextPart_000_01BE54E6.665AF1C0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

The workshop, Advanced Bioinformatics, = taught at UCSD,
has a webpage with course outline, references, = links
and exercises at: =
www.bioinfotech.com/AdvancedBioinformatics.html

Philip = Miller, PhD
BITS: Bioinformational Technical Services

------=_NextPart_000_01BE54E6.665AF1C0-- From owner-software@net.bio.net Thu Feb 04 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!sunqbc.risq.qc.ca!newsfeed.berkeley.edu!newsfeed1.earthlink.net!nntp.earthlink.net!posted-from-earthlink!not-for-mail From: "Liansheng Zheng" Newsgroups: bionet.software Subject: Re: Graphic Output for Genetic Linkage Map, Graphical Genotypes and QTL Plot on PCs Date: Fri, 5 Feb 1999 14:05:32 -0800 References: <004501be5048$a9822a60$8ce65dc6@pbgb-up3.irri.cgiar.org> X-Posted-Path-Was: not-for-mail X-Priority: 3 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.0810.800 X-ELN-Date: 5 Feb 1999 22:07:09 GMT X-ELN-Insert-Date: Fri Feb 5 14:15:03 1999 Organization: EarthLink Network, Inc. X-Newsreader: Microsoft Outlook Express 5.00.0810.800 X-MSMail-Priority: Normal Lines: 96 NNTP-Posting-Host: gatekeeper.ceres-inc.com Message-ID: <79fq2d$j4l$1@fir.prod.itd.earthlink.net> It sound a very interesting program. Would you let my try it? Liansheng Shen Lishuang wrote in message news:004501be5048$a9822a60$8ce65dc6@pbgb-up3.irri.cgiar.org... > >To all: > >I have just written a program, Mapplotter, which can be used to >get graphic output on PC computer. Mapplotter is primarily >designed to plot Genetic Linkage Map, Graphical Genotypes and draw >QTL plot according to results from other programs. It also bear a >picture viewer module for browsing different formats of image >files and a Rich Text Editor module for viewing and modifying data >and result files.. > > >Mapplotter Version 1.1 has the below functions: > >1. Drawing genetic maps, graphical genotypes and QTL plots, drawn >maps are saved as 256-color bitmap files. > >2. It lets you specify the scale on both X-axis and Y-axis. Marker >names are printed in their exact position on map. > >3. For graphical genotypes, it works for DH, RIL, BC and F2 >populations at present. Regions from different parents are show >in different colors and fillstyles. It also give genome ratio of >each plant in "genome ratio.txt" file. > >4. Drawing multiple plants (for graphical genotypes ) or traits >(for QTL plots) in one run. > >5. For QTL plots, it can draw a single trait a time or up to 3 >traits a time. You can choose to draw QTL analysis mode of SIM, >CIM or both on one plot. It also enables you choose to show the >sign of additive effects on QTL plots. > >6. For QTL plot, three QTL result formats are supported now. Two >of them are the same as in QTLCartographer (Zmapqtl.exe result >files and Preplot.exe result files) from North Carolina State >University. Other format can also be added on request. It lets you >choose using LOD score or liklihood ratio (LR) for your own QTL >result file and centiMorgan (cM) or Morgan (M) for your map data >file. > >7. For genetic map data , two formats are supported. One is the >same as in QTLCartographer, the other format can be easily >modified from Mapmaker/EXP output file. > >8. Built-in image viewer enables you quickly browse through your >maps. It can view bitmap, metafile and icon files. It also enables >you do simple editing of the drawn maps. > >9. Built-in image viewer can display the map position and LOD >score of any point in your QTL plots by simply clicking and moving >mouse on the drawn maps. > >10. Most commands are self-evident. Besides, you can also get >hints for some of them by placing mouse cursor on them. > > > >Mapplotter is a Windows 95 program and is freely available for >acedemic use. More functions will be added in future. Please give >it a try and test it. For QTL plotting, more data format for QTL >results can be added upon request. > >For details and how to getting the program, please contact with >the author. > > >Best regards, > > >Lishuang Shen >Project Scientist >Plant Breeding, Genetics and Biochemistry Division >International Rice Research Institute (IRRI) >P.O. Box 3127 >Makati Central Post Office (MCPO) >1271 Makati City >Philippines > >Tel: (63-49)5360672 (home) or (63-2) 8450563-local 540 (Office) >Fax: (63-2)-8450606 or (63-2)-8450563 >Email: lshen@irri.cgiar.org > > > > > > From owner-software@net.bio.net Fri Feb 05 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!netnews.com!newspeer1.nac.net!newsfeed.concentric.net!global-news-master From: John Doe Newsgroups: bionet.software Subject: Re: DNA sequence analysis for Mac Date: 06 Feb 1999 15:05:43 PST Organization: /dev/null Lines: 26 Message-ID: <36BCCD0E.4CFB@aol.com> References: <36B31D13.7366F38E@icr.ac.uk> <36B5FAE3.875ECC6E@chollian.net> Reply-To: jdoe@aol.com NNTP-Posting-Host: ts004d05.nyc-ny.concentric.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.04 (Win95; I) Edwin ten Dam wrote: > > In article <36B5FAE3.875ECC6E@chollian.net>, Senovia von Perle > wrote: > > >There are several softwares for DNA sequence analysis... > >MacDNAsis by Hitachi software... > >MacVector by Oxford... > >Sequencher... > >MacStar... > > Macvector is very nice. The price is rediculous though: A very outrageous > 1800 pounds! I can't see many University labs forking out that sort of > money. Why there isn't an academic discount I can't understand. > > cheers, > > Edwin > > -- > Edwin ten Dam etd@bigfoot.com > School of Biomedical Sciences - University of St Andrews > Biomolecular Sciences Bldng, North Haugh, St Andrews, KY16 9ST U.K. > Phone: +44 1334 463404 - Fax: +44 1334 462595 Why don't you try Vector NTI? (www.informaxinc.com) I believe they have a free demo version available for download. From owner-software@net.bio.net Sat Feb 06 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!rill.news.pipex.net!pipex!newsfeed.ecrc.net!newsfeed00.btx.dtag.de!newsfeed01.btx.dtag.de!newsmm00.btx.dtag.de!news.btx.dtag.de!not-for-mail From: ErnstLudwig@t-online.de (Ernst-Ludwig Brust) Newsgroups: bionet.software Subject: Institut f. Bioinformatik Südbaden (IBiSBaden) Date: Sun, 07 Feb 1999 11:39:49 +0100 Lines: 11 Message-ID: <36BD6D75.691A@t-online.de> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news02.btx.dtag.de 918384206 22065 0762162063-0001 990207 10:43:26 X-Complaints-To: abuse@t-online.de X-Sender: 0762162063-0001@t-online.de X-Mailer: Mozilla 3.01Gold [de]C-DT (Win95; I) Betr.: Institut f. Bioinformatik Südbaden (IBiSBaden) hier: Gründung einer Beratungsfirma Ich, Dipl. Math., Dipl. Inf. mit Grundwissen in Immunologie und molekularer Genetik, möchte gerne mit Interessenten aus der "Bio-Branche" eine Beratungsfirma für o.g. Thema gründen. Wer macht mit ? Ernst-Ludwig Brust Birkenweg 36 79589 Binzen From owner-software@net.bio.net Sat Feb 06 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!spring.edu.tw!serv.hinet.net!netnews.hinet.net!news From: "666" Newsgroups: bionet.software Subject: =?big5?B?pKOs3aVpsaQsrN2kRrqhqKynQaq6v/qlXQ==?= Date: Sat, 6 Feb 1999 23:53:16 +0800 Organization: DCI HiNet Lines: 727 Message-ID: <79hqg2$f4r@netnews.hinet.net> NNTP-Posting-Host: h25.s111.ts30.hinet.net Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_008F_01BE522B.DDD44520" X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_008F_01BE522B.DDD44520 Content-Type: text/plain; charset="big5" Content-Transfer-Encoding: quoted-printable =A4=A3=AC=DD=A5i=B1=A4,=AC=DD=A4F=BA=A1=A8=AC=A7A=AA=BA=BF=FA=A5] $ =A5=FD=AC=DD=B3=CC=AB=E1=AD=B1 $ = 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$=20 =A7A=A9=CE=B3\=B7|=A5H=AC=B0=B3o=A5u=ACO=AD=D3=C4F=A4H=AA=BA=BE=BB=C0Y=A1= A=A5=FD=ABe=A7=DA=AC=DD=A8=EC=C3=FE=A6=FC=AA=BA=ABH=A5=F3=AE=C9=A1A=A4]=B4= =BF=A6=B3=B3o=BA=D8=B7Q=AAk=A1A=A6=FD
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$=20 =AB=CA=B8=CB=A6=B3100=A4=B8=B2{=AA=F7=AA=BA=ABH=A1A=B5=A5=A9=F3=BB=A1=A1A= =A7=DA=A4w=B8g=C1=C8=A6^=A7=DA=A9=D2=A7=EB=B8=EA=AA=BA=AA=F7=C3B=A1A=C1=D9= =A5~=A5[700=A4=B8=AA=BA=A6=AC=A4J=A1C
$=20 =B2=C4=A4G=AD=D3=C2=A7=AB=F4=AB=E1=A1A=A7=DA=AA=BA=A6=AC=A4J=A7=F3=C5=E5=A4= H=A1A=B3=BA=B5M=A6=AC=A8=EC=A4T=A4Q=A4=BB=AB=CA=AA=BA=ABH=A1]=A4]=B4N=ACO= 3600=A1^=A1A
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$=20 =B4=B1=C5K=BE=A6=A1I=B2=A6=B3=BA=A4H=ACO=B7R=BF=FA=AA=BA=B0=CA=AA=AB.=A6=B3= =BF=FA=BD=D6=A4=A3=B7Q=ADn=A1I=A1I=B1z=BB=A1=ACO=B6=DC=A1I
$ = =A6b=A4G=AD=D3=A4=EB=AB=E1=A7=DA=A4S=C1=C8=B6i101000=A4=B8=A1A=A7=EB=B8=EA= =A9=EA=B9S=B2v=A4=A7=B0=AA=A1A=B3s=AA=D1=B2=BC=B3=A3=B1=E6=A4=A7=B2=F6=A4= =CE=A1C
$=20 =AB=E1=A8=D3=A4S=C2_=C2_=C4=F2=C4=F2=A6=AC=A8=EC=BF=FA=A1A=A7=DA=AFu=AA=BA= =AB=DC=B0=AA=BF=B3=A1A=A6]=AC=B0=BE=C7=B6O=A9M=A5=CD=AC=A1=B6O=A5=FE=A6=B3= =B5=DB=B8=A8=A4F=A1C
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:=20 =C5=A5=A7=DA=BB=A1=A7=B9=A6=DB=A4v=AA=BA=BF=CB=A8=AD=B8g=BE=FA=A1A=A7A=A4= @=A9w=A4]=C5D=C5D=B1=FD=B8=D5=BD}=A1I
: = =B3o=BA=D8=A7=EB=B8=EA=A4=E8=AAk=AB=DC=C2=B2=B3=E6=A1A=AD=BA=A5=FD=A7A=A5= =B2=B6=B7=AD@=B5=DB=A9=CA=A4l=AC=DD=A7=B9=A7=DA=A7Y=B1N=A7i=B6D=A7A=AA=BA= =A8=E2=A5=F3=A8=C6=A1]=B3=CC=A6n=A7=E2=A5=A6=A6C
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:=20 =A5X=A8=D3=A1^=A1G
: = =A2=B0.=B3o=AD=D3=ADp=B5e=AA=BA=B9=EA=A6=E6=A4=E8=AAk=A1C
: = =A2=B1.=B3o=AD=D3=ADp=B5e=A5i=A6=E6=AA=BA=AD=EC=A6]=A1C
: = 1.=B3o=AD=D3=ADp=B5e=AA=BA=B9=EA=A6=E6=A4=E8=AAk
:  =20 =A2=CF.=B7=C7=B3=C6=A7=F7=AE=C6=A1G=A4=AD=AD=D3=BC=D0=B7=C7=ABH=AB=CA=A1B= =A4=AD=B1i=A4=AD=A4=B8=AA=BA=B6l=B2=BC=A1B=A4=AD=B1i=C3C=A6=E2=AB=DC=B2`=AA= =BA=AF=C8
:    =20 =A1]=ADn=AF=E0=A7=E2=A2=B0=A2=AF=A2=AF=A4=B8=A5]=A6=ED=A1A=B5L=AAk=AC=DD=A8= =A3=AA=BA=B2`=A6=E2=A1^=A1B=A4=AD=B1i=ABK=B1=F8=AF=C8=A1C
:  = ;=20 =A2=D0.=A4=E8=AAk=A1G=A6b=A8C=B1i=ABK=B1=F8=AF=C8=A4W=BCg=B5=DB=A1y=BD=D0= =B1N=A7=DA=A9=F1=A4J=A7A=AA=BA=B6l=BB=BC=A6W=B3=E6=A4=A4=A1z=A1F=B1N=A2=B0= =A2=AF=A2=AF=A4=B8=A5=CE=B2`
:=20 =A6=E2=AF=C8=A5]=B0_=A8=D3=A1A=A4=C0=A7O=A9=F1=A4J=A8C=AD=D3=ABH=AB=CA=A4= =A4=A1]=A4@=A9w=ADn=C5=FD=A2=B0=A2=AF=A2=AF=A4=B8=B5L=AAk=B3Q=B3z=B5=F8=A1= A=A7_=ABh=AEe=A9=F6
: = =B3Q=A4=A3=A8v=A4=A7=AE{=AE=B3=A8=AB=A1^=A1C
:  =20 =A2=D1.=B1N=B3o=A4=AD=AB=CA=ABH=A4=C0=A7O=B1H=B5=B9=A5H=A4U=AA=BA=A4=AD=AD= =D3=A4H=A1]=AA`=B7N=A1G=A4=A3=A5i=A5H=C0H=ABK=B1H=A1^=A1G
:  = ;     =20 1.=AAL=A9=FA=BC=DD  = =A5x=A4=A4=BF=A4=AFQ=A4=E9=B6m=A5_=A8=BD=A7=F8=B7=CB=ABn=B8=F463-2=B8=B9&= nbsp; =B6l=BB=BC=B0=CF=B8=B9=20 414
:        = 2.=AAL=B5=D7=AA=F8 =20 =B0=AA=A5=AB=B7=A3=B1=EA=B0=CF=AB=E1=A9=F7=B8=F4108=AB=D115=B8=B9 &n= bsp; =B6l=BB=BC=B0=CF=B8=B9=20 811
:        = 3.=AAL=B4=AD=AA@ =20 =B0=AA=B6=AF=BF=A4=A9=A3=A4s=C2=ED=A9=A3=A4s=B8=F4287=B8=B9   = =B6l=BB=BC=B0=CF=B8=B9=20 820
:        = 4.=B3=AF=ABT=B3=C7  = =ABn=A7=EB=BF=A4=A6=CB=A4s=C2=ED=B6=B3=AAL=B8=F4=A4G=AB=D1=A4Q=A4T=B8=B9 = =B6l=BB=BC=B0=CF=B8=B9 = 557
:        = 5.=B1i=A5=C3=BE=CB =20 =A5x=A5_=A5=AB=AAF=B5=D8=B5=F3=A4@=ACq22=AB=D1=A4Q=A4K=A7=CB2=B8=B93=BC=D3=    =20 =B6l=BB=BC=B0=CF=B8=B9112        =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;      =20 (=B0O=B1o=BCg=B6l=BB=BC=B0=CF=B8=B9  = =A7_=ABh=B6l=A7=BD=B1N=A9=B5=AA=F8=A4u=A7@=A4=D1=B3=E1!)
:  = =A2=D2.=A7=F3=A7=EF=A6a=A7}=A1G
:=20 =A1@=A1@=B1H=A7=B9=ABH=AB=E1=A1A=A6A=B3z=B9L=B9q=B8=A3=B1N=A4W=AD=B1=B2=C4= =A4@=AD=D3=A4H=AA=BA=A6W=A6r=BD=F0=B1=BC=A1A=A8=C3=A8=CC=A7=C7=B1N=A5|=AD= =D3=A4H=AA=BA=A6W=A6r=A9=B9=A4W
:    =20 =B2=BE=A4G=B2=BE=A8=EC=A4@=A1F=A4T=B2=BE=A8=EC=A4G=A1F=A5|=B2=BE=A8=EC=A4= T=A1F=A4=AD=B2=BE=A8=EC=A5|=A1^=A1A=A6=D3=B2=C4=A4=AD=AD=D3=BCg=A4W=A7A=AA= =BA=A6W=A6r=A1B=A6a=A7}
:    =20 =A1A=ADn=AA`=B7N=A6a=A7}=ACO=A5=BF=BDT=AA=BA=A1A=A7_=ABh=A7A=B7|=A6=AC=A4= =A3=A8=EC=ABH=B3=E1=A1I
:  =20 =A2=D3.=A5=E1=A4J=B7s=BBD=B8s=B2=D5=A1G=A4=E5=B3=B9=A4=A4=B6=C8=BB=DD=AD=D7= =A7=EF=A1u=A2=D2=A1B=A7=F3=A7=EF=A6a=A7}=AA=BA=B3=A1=A5=F7=A1v=A9=D2=B4=A3= =A8=EC=AA=BA=B3=A1=A5=F7=A1A=ABe=AD=B1
:     = =20 =A9=D2=BB=A1=AA=BA=B8g=C5=E7=B3=A1=A5=F7=A1A=A7A=A5i=A5H=AE=DA=BE=DA=A6=DB= =A4v=AA=BA=B9=EA=AAp=B0=B5=C2=B2=A9=F6=A7=F3=A7=EF=A1A=A8=E4=A5L=AA=BA=B3= =A1=A5=F7=B3=CC=A6n=ABO=AB=F9=AD=EC
=AA=AC
:    = ; =20 =A1A=B5M=AB=E1=A7A=A5=B2=B6=B7=B1N=ABH=A5=F3=A6=DC=A4=D6=A4=BD=A7G=A6b250= =AD=D3=B7s=BBD=B0Q=BD=D7=B0=CF
:    =20 =A1]=B3=CC=A4=D6=ADn=A6=B3=A8=E2=A6=CA=AD=D3=B0Q=BD=D7=B0=CF=A1A=A5=FE=A5= @=AC=C9=AC=F9=A6=B325000=AD=D3=B7s=BBD=B0Q=BD=D7=B0=CF=A1C)
: &nb= sp;    =20 =A1=AF=AA`=B7N=A1G=A7A=A9=D2=A4=BD=A7G=A5X=A5h=AA=BA=B7s=BBD=B0=CF=B6V=A6= h=A1A=B1z=B1o=A8=EC=AA=BA=A6^=F5X=B6V=A6h=A1C
:    = ;  =20 =ADY=A4=A3=AA=BE=A6p=A6=F3=A4=BD=A7G=A8=EC=B7s=BBD=B0=CF=A1A=B1z=A5i=A5H=B7= =D3=A4U=A6C=AA=BA=A4=E8=AAk=A7@=A1G
:  = =A8=CF=A5=CE=BA=F4=B4=BANETSCAPE = NAVIGATOR=AA=BA=A8=CF=A5=CE=AA=CC=A1G
:=20 =A1]=A2=B0=A1^=A5=FD=A5=B4=B6}NETSCAPENEWS=A1A=A6A=A6b=BA=F4=B4=BA=C2s=C4= =FD=BE=B9=A4=A4=B1q=A5\=AF=E0=BF=EF=B3=E6=A4=A4=A5=FD=BF=EF=A8=FAWINDOWS=A1= A=B1=B5=B5=DB
=A6A
:      =20 =BF=EF=A8=FANETSCAPENEWS=A1A=A7Y=A5i=B1=D2=B0=CANETSCAPENEWS=A1D=B5M=AB=E1= =C2I=A8=FA=B3=CC=A5=AA=C3=E4=AA=BA=AB=F6=B6s
=A1ePOSTNEW
: &nb= sp;    =20 S=A1f=A6=B9=AE=C9=B7|=A5X=B2{=A4@=AD=D3=BDs=BF=E8=B7s=A4=E5=B3=B9=AA=BA=B5= =F8=B5=A1=A1D
: = =A1]=A2=B1=A1^=AC=B0=A7A=AA=BA=A4=E5=B3=B9=BF=EF=A4@=AD=D3=A7l=A4=DE=A4H=AA= =BA=BC=D0=C3D=A1D
:=20 =A1]=A2=B2=A1^=B1N=A7A=A5=D8=ABe=AC=DD=A8=EC=AA=BA=B3o=BDg=A4=E5=B3=B9COP= Y=B5M=AB=E1PASTE=A8=EC=B0T=AE=A7=C4=E6=A1A=A4=BA=B7=ED=B5M=A7A=A5i=BEA=B7= =ED=AA=BA=AD=D7=A7=EF=B3o
=BDg
:=20 =A4=E5=B3=B9(=A7A=A5=B2=B6=B7=A7=E2=A7A=AA=BA=A6W=A6r=A4=CE=A6a=A7}=A5[=A6= b=A4=E5=B3=B9=AA=BA=B2=C4=A4=AD=A6=EC=A1]=A7=E2=B2=C4=A4@=A6=EC=A5h=B1=BC= =A1^=A1A=A8=C3=B1N=B3=D1=A4U=AA=BA=A4=E5
=B3=B9
:=A1]=A7A=A5=B2=B6=B7= =A7=E2=A7A=AA=BA=A6W=A6r=A4=CE=A6a=A7}=A5[=A6b=A4=E5=B3=B9=AA=BA=B2=C4=A4= =AD=A6=EC=A1]=A7=E2=B2=C4=A4@=A6=EC=A5h=B1=BC=A1^=A1A=A8=C3=B1N=B3=D1=A4U= =AA=BA=A5|=AD=D3=A4H
=AA=BA
:=20 =A6W=A6r=A4=CE=A6a=A7}=A9=B9=A4W=B2=BE=A4@=A6=EC=A1D
: = =A1]=A2=B3=A1^=B7=ED=A7A=A7=E2=BE=E3=BDg=A4=E5=B3=B9=A5=B4=A6n=A9=CECOPY=A6= n=A4=A7=AB=E1=A1A=C2I=BF=EF=A1eSEND
:=20 NOW]=AB=F6=B6s=A4W=A4=E8=AA=BA=A1eSAVEAS=A1f.=A6b=A7A=C0x=A6s=A4=A7=ABe=A4= d=B8U=A4=A3=ADn=B1N=A4=E5=B3=B9=B1H=A5X=A5h=A1D=A1]=B3o=BC=CB=A7A=A4~=A4=A3= =A5=CE
=AD=AB
:=20 =BD=C6=A5=B4=AC=DB=A6P=A4=BA=AEe=A2=B1=A2=B4=A2=AF=A6=B8=A1^
:
:=A1= ]=A2=B4=A1^=B2{=A6b=A7A=A4w=B1N=ADn=B1H=B0e=AA=BA=A4=E5=B3=B9=A4=BA=AEe=C0= x=A6s=A6n=A1A=B6}=A9l=A8=D3=B1H=B0e=A7A=AA=BA=B2=C4=A4@=BDg=A4=E5=B3=B9=A7= a=A1I=C2I=BF=EF=A5=AA
=A4W
:=20 =A4=E8=A1eSENDNOW=A1f=AA=BA=AB=F6=B6s=A1D
:=A1]=A2=B5=A1^=B2{=A6b=A7A=AD= n=B6}=A9l=B1H=B0e=A2=B1=A2=B4=A2=AF=AB=CAPOST=A4F=A1A=BF=EF=BE=DC=A5=F4=A4= @=B7s=BBD=B0Q=BD=D7=B0=CF=A1A=A6A=C2I=BF=EF
:=A1ePOSTNEWMESSAGE=A1f=AB= =F6=B6s=A1A=C0=B0=A7A=AA=BA=A4=E5=B3=B9=A8=FA=AD=D3=A4=DE=A4H=AA`=A5=D8=AA= =BA=BC=D0=C3D=B5M=AB=E1=B2=BE=A8=EC=AD=E8SAVE=AA=BA=A4=E5=B3=B9=A5=BB
= =A4=E5
:=20 =AA=BA=B3=A1=A5=F7=A1A=AB=F6=A6=ED=B7=C6=B9=AB=A5=AA=C1=E4=A4=A3=A9=F1=A1= A=B1N=BE=E3=AD=D3=A4=E5=B3=B9=A4=CF=A5=D5=B0_=A8=D3=A1A=B5M=AB=E1=A5=CECO= PY=A9MPASTE=B1N=BE=E3=BDg=A4=E5=B3=B9
=AB=FE
:=20 =B3=C6=A6=DC=B7s=AA=BA=A4=E5=A6r=AA=BA=B5=F8=B5=A1=A7Y=A5i=A1D=B2{=A6b=B6= }=A9l=B3=B0=C4=F2=B6K=A9=B9=A4=A3=A6P=AA=BA=A2=B1=A2=B4=A2=AF=AD=D3=B7s=BB= D=B0Q=BD=D7=B0=CF=A7a=A1I
: = =A8=CF=A5=CE=AA=BA=B1=B4=C0I=AEa=C2s=C4=FD=BE=B9Microsoft Internet=20 Explorer:=A4=E8=AAk=A4]=ACO=A4@=BC=CB=AA=BA=C2=B2=B3=E6=A1A=AB=F6=A6=ED=B7= =C6
: = =B9=AB=A5=AA=C1=E4=A4=A3=A9=F1=A1A=B1N=BE=E3=AD=D3=A4=E5=B3=B9=A4=CF=A5=D5= =B0_=A8=D3=A1A=B5M=AB=E1=A6P=AE=C9=AB=F6=B5=DB=A1eCTRL=A1f=A4=CE=A1e=A2=D1= =A1f=C1=E4=B1N=BE=E3=BDg=A4=E5=B3=B9=AB=FE
=A8=A9
:=20 =A8=EC=B6K=C3=AF=A1D=A6=B9=A6A=B1N=A5=BB=A4=E5=A6C=A6L=A5X=A8=D3=A1D=B3o=BC= =CB=A7A=B4N=A6=B3=A4@=A5=F7=A7A=B4=BF=B8g=B1H=A5X=B7s=A5x=B9=F4=A2=B0=A2=AF= =A2=AF=A4=B8=AA=BA=A6W=B3=E6
=A4F=A1D
: = =B0O=B1o=B1N=A7A=AA=BA=A6W=A6r=A6a=A7}=A5[=A6b=A6W=B3=E6=AA=BA=B3=CC=AB=E1= =A1I
:
:=20 =B3o=BB=F2=A4@=A8=D3=A7A=A5u=BB=DD=ADn=A6b=A7A=B7=C7=B3=C6=B6K=A4=E5=B3=B9= =AA=BA=B0Q=BD=D7=B0=CF=BF=EF=BE=DC=B5o=AA=ED=B7s=AA=BA=A4=E5=B3=B9=A1A=B5= M=AB=E1=A5H=A1eCTRL=A1=CFV=A1f
=B1N
:=20 =A4=E5=B3=B9=A4@=B0_=BB=DD=ADn=A6b=A7A=B7=C7=B3=C6=B6K=A4=E5=B3=B9=AA=BA=B0= Q=BD=D7=B0=CF=BF=EF=BE=DC=B5o=AA=ED=B7s=AA=BA=A4=E5=B3=B9=A1A=B5M=AB=E1=A5= H=A1eCTRL=A1=CFV=A1f=B1N=A4=E5
=B3=B9
:=20 =A4@=B0_=B6K=A1ePASTE=A1f=A5X=A1A=B4N=ACO=B3o=BB=F2=C2=B2=B3=E6=A1A=A7A=A5= u=BB=DD=ADn=BF=EF=BE=DC=A4=A3=A6P=AA=BA=B7s=BBD=B0Q=BD=D7=B0=CF=A1A=B5M=AB= =E1=BF=EF=BE=DC
:=A1ePOST=A1f=B5o=B3=B9=A4=E5=B3=B9=A1D=B5=A5=A7A=B2=DF= =BAD=BE=E3=AD=D3=B9L=B5{=AB=E1=A1A=A8C=B5o=A4@=AB=CA=ABH=A4j=AC=F9=A5u=BB= =DD=ADn=A2=B2=A2=AF=AC=ED=AA=BA=AE=C9=B6=A1=A9O=A1I
:
:=20 (=A2=B0)=A6b=A5=BB=A4=E5=B3=B9=A4W=AD=B1=AA=A9=A5\=AF=E0=A6C=A4W=C2I=BF=EF= =A1e=BDs=BF=E8=A1f=B6=B5=A1A=A6A=C2I=BF=EF=A1e=A5=FE=BF=EF=A1f=A1A=A6=B9=AE= =C9=BE=E3=AD=D3=A4=E5=B3=B9=A4=CF
=A5=D5=A1A
:=20 =A6A=C2I=BF=EF=A1e=BD=C6=BBs=A1f=A1A=ABh=A7=DA=AA=BA=A4=E5=B3=B9=B4N=BD=C6= =BBs=A6b=B1z=AA=BA=B0=C5=B6K=C3=AF=A4W=A1e=A5=D8=ABe=AC=DD=A4=A3=A8=EC=A1= f=A1D=A4]=A5i=A6P=AE=C9=AB=F6
:=A1eCTRL=A1f=A1=CF=A1e=A2=D1=A1f=C1=E4=A1= D=A7=B9=A6=A8=A5H=A4W=B0=CA=A7@=AB=E1
:
:=20 (=A2=B1)=A8=CC=A7=C7=C2I=BF=EF=A1e=B7s=BBD=A1f=A1=D0=A1e = =B6}=B0_=B7s=AA=BA=B7s=BBD=B8s=B2=D5=B6l=A5=F3=A1f=A1A=A6=B9=AE=C9=B1N=A5= X=B2{=B7s=AA=BA=AA=C5=A5=D5=BD=D7
:=20 =BDZ=A1D=A5B=B4=E5=BC=D0=B0=B1=AFd=A6b=ADn=A8D=BF=E9=A4J=B7s=BBD=B8s=B2=D5= =B3B=A1A=A5=D1=A9=F3=A5=BB=A4=E5=AC=B0=A4=A4=A4=E5=A1A=ACG=BE=A8=B6q=B5o=A4= =A4=A4=E5=B0=CF=B8s=B2=D5=B8=FB=A6=B3
=AE=C4=A1D
:
:=20 (=A2=B2)=A6A=A8=CC=A7=C7=C2I=BF=EF=A1e=B7s=BBD=A1f=A1=D0=A1e=BF=EF=BE=DC=B7= s=BBD=B8s=B2=D5=A1f=A1A=A6=B9=AE=C9=A5X=B2{=B3\=A6h=B0Q=BD=D7=B8s=B2=D5=A1= A=A7A=A5i=A5H=A6b=A4W
=A4=E8
:=20 =BF=E9=A4J=B7j=B4M”tw”=AA=BA=C3=F6=C1=E4=A6r=A1A=ABh=A9=D2=A8= =A3=A6C=A5X=AA=BA=B4N=ACO=A5x=C6W=AC=DB=C3=F6=AA=BA=B0Q=BD=D7=B0=CF=A1A=B3= o=AE=C9=B4N=A8=CC=B1z=AD=D3=A4H=BB=DD
=ADn
:=20 =ACD=BF=EF=A8=C3=B1i=B6K=A4=E5=B3=B9=A4F=A1D=A7A=B1N=A6=AC=A8=EC=A8=D3=A6= =DB=A5=FE=BBO=C6W=A6U=A6a=A4D=A6=DC=A9=F3=A5=FE=B2y=A6U=A6a=AA=BA=A6^
= :   =20 =ABH,=A7=C6=B1=E6=AF=E0=A5[=A4J=A7A=AA=BA"=B6l=BB=BC=A6W=B3=E6"= !=A1]=B7=ED=B5M,=BD=D0=B0=C8=A5=B2=BDT=BB{=B1H=B0e=A6a=A7}=AA=BA=A5=BF=BD= T!=A1^=A1@=A1@=A1@
:=A1@
: =20 2.=B3o=AD=D3=ADp=B5e=A5i=A6=E6=AA=BA=AD=EC=A6]
:   &nbs= p;   =20 =A6b=A7A=B5o=A5X250=AB=CA=A4=E5=B3=B9=A4=A4=A1A=B0=B2=B3]=A5u=A6=B3=A4=AD= =AD=D3=A4H=A6^=C0=B3=A7A=AA=BA=A4=E5=B3=B9=A1]=B3o=AD=D3=C1|=A6C=A5=CE=AA= =BA=A4=F1=A8=D2=AC=DB
=B7=ED
:   =20 =A7C=A1^=A1A=B7=ED=A7=DA=AA=BA=A6W=A6r=A6b=B2=C4=A4=AD=A6=EC=AE=C9=A7=DA=C1= =C8=B6i=A4F250=A4=B8=A1C
:       =20 =B2{=A6b=A6^=C0=B3=A7=DA=A4=E5=B3=B9=AA=BA=A4=AD=AD=D3=A4H=A1A=A4]=B4N=AC= O=B1H=B5=B9=A7=DA=B7s=BBO=B9=F4100=A4=B8=AA=BA=B3o=A4=AD=AD=D3=A4H=A4S=A6= U=A6=DB=A6=DC=A4=D6
=B6K
:   =20 =A5X250=AB=CA=A4F=A4=E5=B3=B9=A1A
:      = ; =20 =A6=B9=AE=C9=A7=DA=AA=BA=A6W=A6r=B1N=A4W=B2=BE=A6=DC=B2=C4=A5|=A6=EC=A1F=B0= =B2=B3]=A4]=A5u=A6=B3=A4=AD=AD=D3=A4H=A6U=A6=DB=A6^=C0=B3=B5=B9=A5L=AD=CC= =B3o=A4=AD=AD=D3=A4H(
:   =20 =A4]=B4N=ACO=B3=CC=A6=AD=B1H=BF=FA=B5=B9=A7=DA=AA=BA=A4H)=A1A=A8=BA=A7=DA= =A4S=A6=AC=B6i=A4F=B7s=BBO=B9=F42500=A4=B8=A1A=ADY=B3o=A2=B1=A2=B4=AD=D3=A4= H=A4]=A6U=A6=DB=B6K
=A5X
:   =20 =A4F250=AB=CA=A4=E5=B3=B9=A1A=A6=B9=AE=C9=A7=DA=AA=BA=A6W=A6r=A6b=A6W=B3=E6= =A4=A4=AA=BA=B2=C4=A4T=A6=EC=A1F=ADY=A4]=ACO=A5u=A6=B3=A4=AD=AD=D3=A4H=A6= U=A6=DB=A6^=C0=B3=A5L=AD=CC
=AA=BA
:   =20 =A4=E5=B3=B9=A1A=A8=BA=A7=DA=B1N=A6A=A6=AC=A8=EC=A4F62500=A4=B8=A1A=A6=B9= =AE=C9=B3o125=A4H=A6b=A6U=A6=DB=B6K=A5X250=AB=CA=A4=E5=B3=B9=A1A
:&nbs= p;      =20 =A6=B9=AE=C9=A7=DA=AA=BA=A6W=A6r=A6b=B2=C4=A4G=A6=EC=A1F=A6P=BC=CB=A5L=AD= =CC=A8C=AD=D3=A4H=A4]=A6U=A6=DB=A6=AC=A8=EC=A2=B4=AD=D3=A6^=C0=B3=A1A=A8=BA= =A7=DA=A4S=B1N=A6=AC
=A8=EC
:   =20 12500=A4=B8=A1C
:       =20 =A6P=B2z2625=A4H=A4]=A6U=A6=DB=B6K=A5X250=BDg=A4=E5=B3=B9=A1A=A6=B9=AE=C9= =A7=DA=AA=BA=A6W=A6r=A6b=B2=C4=A4@=A6=EC=A1A=A8=BA=A7=DA=B1N=A6A=A6=AC=A4= J
315200
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------=_NextPart_000_008F_01BE522B.DDD44520-- From owner-software@net.bio.net Sat Feb 06 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.concentric.net!global-news-master From: ketchup*NOSPAM*@cris.com (Ketchup) Newsgroups: bionet.software Subject: GeneDoc version 2.5 (freeware for windows) Date: 07 Feb 1999 14:17:53 PST Organization: Concentric Internet Services Lines: 76 Message-ID: <36be1103.113983@news.cris.com> NNTP-Posting-Host: ts004d01.oak-ca.concentric.net X-Newsreader: Forte Free Agent 1.11/32.235 Please be informed that GeneDoc version 2.5 has been released to the GeneDoc web site: http://www.cris.com/~ketchup/genedoc.shtml Anyone using GeneDoc should upgrade to this version. Significant new features, driven mainly by user input, include: Lots of work on arrangement features: Select a subset of sequences for arrangement. Insert/Delete with Left/Right clicks. Insert/Delete keys for gaps. Additional arrangement functions. Log Odds scoring. DNA to Protein translation for alignments. You can apply gaps from a protein project to a DNA project. Persistant annotation and manual shading. New menus are much more intuitive. Toolbar Tips. Redone help file. Sequence descriptions. Work on sections of an alignment. Enzyme Gel simulation display. Karl Nicholas 2.5 * Made spaces in sequence names a warning. * Fixed bug where loading user files after EMBL files fails. * Fixed bug in Enzyme Report where first cut 1 too short. * Changed Menus Considerably. * Added Toolbar Tips to Toolbars. * Added Function to ReGap DNA Project with Protein Project. * Added Select Ranges to DNA Translation. * Added DNA Frequency reports. * Added Crtl-CR to to opposite arrangement as CR. * Added DNA Translation * Added Insert a single gap in all columns function * Fixed bug causing display of group colors in name seperator. * Added replace data with data from another project. * Changed logodds report to allow to exclude no sequences. * Changed Ins/Del key to work while residue editing. * Added Clear of Manual Comments and Manual Shading. * Added LogOdds alignment scoring. * Changed caret handling a bit. * Added Copy Consensus to clipboard as fasta file function. * Changed toolbar copy button to copy as metafile. * Changed replace to work on whole alignment if nothing selected. * Added Saving of Manual Shading with show/hide config and button. * Added Saving of Comments with show/hide config and button. * Added Quick Find Function with MisMatches and Ins/Deletes. * Added Ins/Del keys to Insert and Delete Gaps always. * Added Right Mouse buttons does opposite of left mouse button in Arrangement modes. * Fixed bug that hangs when export as Text/No Gaps. * Changed user cannot enter spaces into data area. * Added Display '~' as ' ' feature. * Changed Fixed width parameter to be as high as 1000000. * Removed 'Protected First Line' from Titling Facility. * Fixed DNA complement to include ambiguities. * Improved Slide Text routine so it does not unnecessarily grow alignment. * Added Alignment Width Block Size option. * Fixed possible crash when scoring/stats on few sequences. * Added sequence description field. * Added import IUPAC only funtion. * Added Delete Data Columns function. * Added Print Filename and Date with pagenumber. * Fixed manual data input from crashing From owner-software@net.bio.net Sat Feb 06 22:00:00 1999 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!newsfeed1.swip.net!swipnet!rill.news.pipex.net!pipex!news.imp.ch!sibyl!news-sol.swissonline.ch!newsfeed-zh.ip-plus.net!news.ip-plus.net!News.Amsterdam.UnisourceCS!news.otenet.gr!not-for-mail From: "Giorgos Karas" Newsgroups: alt.collecting.stamps.software,alt.comp.software.easter-eggs,alt.comp.software.financial.peachtree,alt.comp.software.njdm,alt.comp.software.tools,alt.med.software,alt.video.dvd.software,bionet.software,bionet.software.acedb,bionet.software.gcg,b Subject: Re: real player files Date: Sat, 30 Jan 1999 00:09:25 -0800 Organization: An OTEnet S.A. customer Lines: 25 Message-ID: <79kgbm$3s4$1@ns1.otenet.gr> References: <78sjof$ele$1@nslave1.tin.it> <78st70$50$1@franklin.ljcrf.edu> NNTP-Posting-Host: thes530-a051.otenet.gr X-Trace: ns1.otenet.gr 918406326 3972 195.167.123.179 (7 Feb 1999 16:52:06 GMT) X-Complaints-To: abuse@otenet.gr NNTP-Posting-Date: 7 Feb 1999 16:52:06 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Xref: biosci bionet.software:22809 bionet.software.acedb:2157 bionet.software.gcg:3403 Or you could track the temporary file in the Windows/temp directory and copy it as the player plays it and then paste it and change its name. you will be left with the file :) of course, you will lose the last 2 seconds or so of the file, since if you copy it midway, only that portion will be copied. so i would suggest, you listen to it once and then copy it a couple of seconds before the end. happy copying and pasting!!! Giorgos Karas Medical Student PS Delete all the other real files in the temp directory, so that you can find which one it is quickly, or keep on pressing the refresh button and see which files increases in size. that is the file you want! Dr. Greg Quinn wrote in message <78st70$50$1@franklin.ljcrf.edu>... >gelso (gelso@removehotmail.com) wrote: >: anyone knows how can i save real player files on hd and play it offline? >: thanx in advance > >Yes, buy the real player plus, which has the extra download function. Note >that this is only possible if the download feature was enabled when the >file was created; there may be (commercial/copyright) reasons why people >won't have enabled download on their real audio/video files. From owner-software@net.bio.net Sun Feb 07 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.gamma.ru!Gamma.RU!newsfeed.cwix.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: jsandidge@sjha.org Newsgroups: bionet.software Subject: motion analsysis software Date: Mon, 08 Feb 1999 15:00:32 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 13 Message-ID: <79mu6b$1po$1@nnrp1.dejanews.com> NNTP-Posting-Host: 170.59.217.217 X-Article-Creation-Date: Mon Feb 08 15:00:32 1999 GMT X-Http-User-Agent: Mozilla/2.0 (compatible; MSIE 3.01; Windows 95) X-Http-Proxy: 1.0 x15.dejanews.com:80 (Squid/1.1.22) for client 170.59.217.217 I work with a group of dysphagia researchers. We are interested in finding out what is new in software for analysising 2 dimensional videofluoroscopic images, for example, distance traveled from one point to another, etc. Also, need to know if most analysis software packages are equipped with a module to first digitize an image originally stored to videotape, or is a digitization software package needed in addition to first capture the taped image? Any help will be greatly appreciated. Thanks, John -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Sun Feb 07 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!usc!newshub.csu.net!news.fullerton.edu!rolltmpxa80937kbbw.fullerton.edu!user From: DEernisse@fullerton.edu (Doug Eernisse) Newsgroups: bionet.software Subject: Re: aligned sequences editing software Date: Sun, 07 Feb 1999 16:59:30 -0800 Organization: CSUF Lines: 37 Message-ID: References: NNTP-Posting-Host: rolltmpxa80937kbbw.fullerton.edu > In article , > tuinen@epoisses.inra.fr (Diederik van Tuinen) wrote: > > >I am looking for a software, hopefully shareware and runing on MacOS, > >allowing to edit aligned sequences - adding or removing gaps - after a > >clustalv run. > Besides the other good suggestions already offered, you might find my "DNA Stacks" software for HyperCard useful. I usually specify NBRF/PIR or Phylip output file types when using ClustalX or ClustalW (Phylip will truncate long sequence labels, however), and then use the "Import Options..." from the Data menu of Aligner stack (one of the "DNA Stacks") to import the alignment. Some of the matching/coloring options might also be of interest, for example, matching to the first sequence and then coloring according to amino acid coding, or amino acid properties, by triplets of DNA. See also, "Align DNA to Proteins" to place gaps in the corresponding DNA file based on the amino acid alignment currently in Aligner. There are some tutorials from within Aligner that will help with the somewhat quirky interface of this stack. I like Seq-Al & SeqPup too but you might find yourself frustrated if much alignment editing is attempted in any of these. Get DNA Stacks (with Aligner) as freeware at http://biology.fullerton.edu/deernisse/dnastacks.html Version 1.0 of the software was released in 1990 and the current '98 version is 1.2. Doug -- Doug Eernisse Department of Biological Science California State University Fullerton, CA 92834-6850 USA From owner-software@net.bio.net Sun Feb 07 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newsfeed.ecrc.net!newsfeed2.ecrc.net!news.siemens.de!news.mch.sbs.de!etsch!korbi From: Korbinian Strimmer Newsgroups: bionet.software Subject: Update: PUZZLE 2.0.1 Date: Mon, 8 Feb 1999 15:10:53 +0100 Organization: Siemens Inc. Lines: 61 Message-ID: NNTP-Posting-Host: etsch.mchp.siemens.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: QUOTED-PRINTABLE X-Sender: korbi@etsch Announcing PUZZLE maintainance release 4.0.1 =20 Korbinian Strimmer =09 Arndt von Haeseler =09 =09 February 1999 PUZZLE is a maximum likelihood program for analysis of molecular sequence data. After 15 months of stable sources the first bug-fix update PUZZLE 4.0.1 is now available. No new features have been added in comparison to version 4.0 but a number of smaller (and also one severe) problems have been resolved. Generally, an update seems to be absolutely necessary if you are using PUZZLE in conjunction with the mtREV-24 matrix. What=B4s new in PUZZLE 4.0.1:=20 - correction of mtREV matrix: wrong likelihood values for this model - fix of the "intree bug": prevents PUZZLE 4.0 from reading some input trees - stringent runtime-compatibility check removed: prevents PUZZLE 4.0 from running on alpha =09 =20 - more accurate gamma distribution: 16 instead of 8 categories, better alpha > 1.0 - update of documentation: mainly address changes - more Unix-like file layout, and - change of licence to GPL PUZZLE 4.0.1 is available (or will soon be available) from: http://members.tripod.de/korbi/puzzle/ http://www.zi.biologie.uni-muenchen.de/~strimmer/puzzle.html ftp://ftp.ebi.ac.uk/pub/software ftp://ftp.pasteur.fr/pub/GenSoft=20 http://iubio.bio.indiana.edu/soft/molbio/evolve=20 ftp://iubio.bio.indiana.edu/molbio/evolve=20 PUZZLE is written in ANSI C. It will run on most computers if compiled by an appropriate C compiler (e.g., gcc). From owner-software@net.bio.net Mon Feb 08 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsgate.cuhk.edu.hk!news.hku.hk!hkusub.hku.hk!not-for-mail From: Xia Xuhua Newsgroups: bionet.software Subject: DAMBE Software package Date: 9 Feb 1999 02:07:39 GMT Organization: The University of Hong Kong Lines: 84 Message-ID: <79o59b$2c81@hkusud.hku.hk> NNTP-Posting-Host: 147.8.145.42 Summary: Comparative sequence analysis and phylogenetics Keywords: Windows, DNA, protein, phylogenetics, molecular sequence X-Newsreader: TIN [UNIX 1.3 release 961025] DAMBE (Data Analysis in Molecular Biology and Evolution) is an integrated software package running on Windows 95 for comparative analysis of molecular data (including nucleotide and amino acid sequence data as well as allele frequency data). The software is available at: http://web.hku.hk/~xxia/software/software.htm The main features are outlined below: --File input with commonly used DNA and protein sequence formats, including MEGA (interleaved and sequential), Pearson/FASTA, ClustalW, IG (IntelliGenetics), GB (GenBank), GCG single-sequence (.GCG) and multi-sequence format(.MSF), Yang's PAML format (interleaved and sequential, but not the one with the G option) and RST format, Kumar's PHYLTEST format, as well as those formats understood by Don Gilbert's READSEQ (which is included for your convenience). One particular strength of the program lies in its versatility with the GenBank (GB) file format - the program can automatically splice out and join CDS, exons, introns, mRNA segments according to the FEATURES table in the GB file. --File conversion between commonly used sequence formats. --Saving subsets of sequences in any of commonly used format. --Many convenient ways of manipulating nucleotide and amino acid sequences. --Many descriptive statistics of molecular sequences. --Generating distance matrices including Jukes and Cantor's (1969) distance, Kimura's (1980) two-parameter distance, Tajima and Nei's (1984) distance, Lake's (1994) paralinear distance, and an entropy-based distance which seems to perform better in phylogenetic reconstruction than other distances based on preliminary studies. --Phylogenetic analyses using distance, maximum parsimony and maximum likelihood methods; resampling statistics (bootstrap and jackknife). --Graphically display phylogenetic trees (including consensus tree) and topology manipulation. --For pair-wise differences, one particular strength of the program lies in its ability to count the differences between neighboring nodes along a phylogenetic tree if the tree structure is provided. For example, the BASEML program in the PAML package can reconstruct ancestral sequences when a topology is given. The output file from BASEML, called rst by default, contains the tree topology as well as the reconstructed sequences. DAMBE can read the RST file directly and count pair-wise differences in nucleotide, amino acid and codon sequences between neighboring nodes along the phylogenetic tree. --Fit the Poisson and negative binomial distributions to nucleotide, amino acid, and codon substitutions along the DNA sequences. --Computing expected pattern of codon substitution given a genetic code (e.g., mammalian mitochondrial), with or without adjustment for codon frequencies. All 12 different genetic codes have been implemented. --Quantifying the extent of substitution saturation in nucleotide sequences for one to decide whether to include or exclude certain nucleotide sites in phylogenetic reconstruction --Plotting amino acid properties (chemical composition along the side chain, volume, polarity, polar requirement, hydropathy, aromaticity, and isoelectric point) along sequences --Computing an entropy-based measure of variability over sites and plot the variability along the sequences. --Special computational tools for analyzing the effect of DNA methylation on molecular evolution of nucleotide sequences. The strength of DAMBE is not in what it can do, but in the way it does it, which I believe will save many researchers many hours. Best. Xuhua =================================================================== Xuhua Xia | Tel: (852) 2857 8239 (lab) Assistant Professor | Tel: (852) 2975 5629 (office) Department of Ecology & Biodiversity| Fax: (852) 2517 6082 The University of Hong Kong | Email: xxia@hkusua.hku.hk Pukfulam Road | WWW: http://web.hku.hk/~xxia Hong Kong | =================================================================== From owner-software@net.bio.net Mon Feb 08 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.ecrc.net!newsfeed2.ecrc.net!news.siemens.de!news.mch.sbs.de!etsch!korbi From: Korbinian Strimmer Newsgroups: bionet.software Subject: treetool for Linux Date: Tue, 9 Feb 1999 16:35:07 +0100 Organization: Siemens Inc. Lines: 17 Message-ID: NNTP-Posting-Host: etsch.mchp.siemens.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: korbi@etsch Does anybody run "treetool" by Mike Maciukenas (from the Ribosomal RNA Database project) on Linux? I have tried to compile the v.2.0.2 sources and succeeded even to link (with the xview libs) but still it doesn't work ("normal" termination with an error - no core dumbs)... :( Any hints (maybe also to other tree manipulation software that runs on Linux)? Korbinian -- Korbinian Strimmer -- http://members.tripod.de/korbi/ From owner-software@net.bio.net Mon Feb 08 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.ecrc.net!firehose.mindspring.net!firehose.mindspring.com!not-for-mail From: agkistrodon@mindspring.com (Copperhead) Newsgroups: bionet.software Subject: IACUC Experiences Date: Mon, 08 Feb 1999 18:24:41 GMT Organization: MindSpring Enterprises Lines: 13 Message-ID: <36bf2bd9.1938593@news.mindspring.com> Reply-To: agkistrodon@mindspring.com NNTP-Posting-Host: d1.56.a2.01 X-Server-Date: 9 Feb 1999 18:26:17 GMT X-Newsreader: Forte Free Agent 1.1/32.230 I have been asked to connect with various news groups that might have experience with Institutional Animal Care and Use Committees that have experience with the use of Lotus Notes to discover how it is used and what problems you have had with it, if any. If anyone here has such experience, please contact me by e-mail as the server at work does not allow access to many news groups. James L. Sutton Sutton.james@epamail.epa.gov or Agkistrodon@mindspring.com From owner-software@net.bio.net Mon Feb 08 22:00:00 1999 Path: biosci!CMMT.UBC.CA!francis From: francis@CMMT.UBC.CA (Francis Ouellette) Newsgroups: bionet.software Subject: Re: DNA sequence analysis for Mac Date: 8 Feb 1999 22:33:23 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <36BFB74B.B0D12DC5@compusmart.ab.ca> NNTP-Posting-Host: net.bio.net >You might be interested in GeneTool (http://www.biotools.com). The >interface is really nice and it's pretty cheap (especially with the >academic discount). > >-- >Andrew Gardner andrewg@compusmart.ab.ca > http://www.compusmart.ab.ca/andrewg/ Andrew, I'm assuming that even though you ar efrom Alberta (Edmonton?), that you have no commercial invesments or ties with Genetools, and that you are simply a happy user of this product, right? As you may know, advertising is really not accepted on this newsgroup, (and other BIOSCI newsgroups (although plenty do it). If you are indeed simply a happy user, it's a good practice to say so! cheers, f. (a happy user of the internet, with no invesment in it :-) -- | B.F. Francis Ouellette tel: (604) 875-3815 | | Director, Bioinformatics Core Facility fax: (604) 875-3800 | | Centre for Molecular Medicine and Therapeutics, UBC, Canada | | francis@cmmt.ubc.ca | From owner-software@net.bio.net Mon Feb 08 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!remarQ73!supernews.com!remarQ.com!remarQ69!not-for-mail From: Andrew Gardner Newsgroups: bionet.software Subject: Re: DNA sequence analysis for Mac Date: Mon, 08 Feb 1999 21:19:23 -0700 Organization: Posted via RemarQ, http://www.remarQ.com - Discussions start here! Lines: 11 Message-ID: <36BFB74B.B0D12DC5@compusmart.ab.ca> References: <36B31D13.7366F38E@icr.ac.uk> <36B5FAE3.875ECC6E@chollian.net> NNTP-Posting-Host: 207.229.35.93 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: 918533700 OO9TMNNMC235DCFE5C usenet87.supernews.com X-Complaints-To: newsabuse@remarQ.com X-Mailer: Mozilla 4.5 [en] (Win95; U) X-Accept-Language: en > Macvector is very nice. The price is rediculous though: A very outrageous > 1800 pounds! I can't see many University labs forking out that sort of > money. Why there isn't an academic discount I can't understand. You might be interested in GeneTool (http://www.biotools.com). The interface is really nice and it's pretty cheap (especially with the academic discount). -- Andrew Gardner andrewg@compusmart.ab.ca http://www.compusmart.ab.ca/andrewg/ From owner-software@net.bio.net Mon Feb 08 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.gtei.net!firehose.mindspring.com!not-for-mail From: agkistrodon@mindspring.com (Copperhead) Newsgroups: bionet.software Subject: IACUC Experiences Date: Mon, 08 Feb 1999 23:12:58 GMT Organization: MindSpring Enterprises Lines: 13 Message-ID: <36bf6f6e.1701404@news.mindspring.com> Reply-To: agkistrodon@mindspring.com NNTP-Posting-Host: d1.56.a7.4e X-Server-Date: 9 Feb 1999 23:14:34 GMT X-Newsreader: Forte Free Agent 1.1/32.230 I have been asked to connect with various news groups that might have experience with Institutional Animal Care and Use Committees that have experience with the use of Lotus Notes to discover how it is used and what problems you have had with it, if any. If anyone here has such experience, please contact me by e-mail as the server at work does not allow access to many news groups. James L. Sutton Sutton.james@epamail.epa.gov or Agkistrodon@mindspring.com From owner-software@net.bio.net Mon Feb 08 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!woodstock.news.demon.net!demon!news.demon.co.uk!demon!cammol1.demon.co.uk!r_grant From: r_grant@see.sig.for.address (Richard P. Grant) Newsgroups: bionet.software Subject: Re: DNA sequence analysis for Mac Date: Tue, 09 Feb 1999 08:54:10 +0000 Organization: post does not necessarily reflect the views of Cambridge Molecular Distribution: world Message-ID: References: <36BFB74B.B0D12DC5@compusmart.ab.ca> Reply-To: rgrant@netscape.net NNTP-Posting-Host: cammol1.demon.co.uk X-NNTP-Posting-Host: cammol1.demon.co.uk:212.228.79.177 X-Trace: news.demon.co.uk 918550460 nnrp-12:754 NO-IDENT cammol1.demon.co.uk:212.228.79.177 X-Complaints-To: abuse@demon.net X-Newsreader: MT-NewsWatcher 2.4.4 X-No-ahbou: YES X-No-Archive: YES X-Face: E%wu[EoEhNnjFG!0[ 7cH@VuxC//iy$!n-+bh9Q`+SHW@&}E.&Ly(y'Tvrd5amG/o35>c3zF6QvXX, francis@CMMT.UBC.CA (Francis Ouellette) wrote: >As you may know, advertising is really not accepted on this newsgroup, >(and other BIOSCI newsgroups (although plenty do it). Indeed. Although given the context of the thread - I wonder how the etiquette applies here? Perhaps if I were selling such software (which I'm not) then I should email the interested poster(s) directly, but then that is treading a fine line between UCE and UI . . . Meantime, *unsolicited* advertisers go straight into my kill files, so I never see them again. R -- Richard P. Grant MA DPhil rgrant at cmtech.co.uk 'Mac users exhibit many of the behaviours of minority groups in wider society, and exist under much the same pressure of casual bigotry' - JJS in uk.comp.sys.mac From owner-software@net.bio.net Tue Feb 09 22:00:00 1999 Sender: thomas@beagle.bmc.uu.se To: Korbinian Strimmer Newsgroups: bionet.software Subject: Re: treetool for Linux References: Mime-Version: 1.0 (generated by tm-edit 7.108) Content-Type: text/plain; charset=US-ASCII From: Thomas Sicheritz Date: 10 Feb 1999 09:51:42 +0100 Message-ID: Lines: 36 X-Newsreader: Gnus v5.5/XEmacs 20.4 - "Emerald" NNTP-Posting-Host: beagle.bmc.uu.se X-Trace: 10 Feb 1999 09:52:18 +0100, beagle.bmc.uu.se Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newsfeed1.swip.net!swipnet!purple!newsfeed.sunet.se!news01.sunet.se!news99.sunet.se!newsfeed.uu.se!beagle.bmc.uu.se Korbinian Strimmer writes: > Does anybody run "treetool" by Mike Maciukenas > (from the Ribosomal RNA Database project) > on Linux? I have tried to compile the v.2.0.2 sources > and succeeded even to link (with the xview libs) > but still it doesn't work ("normal" termination > with an error - no core dumbs)... :( Treetool will only run with 8bpp (256 color mode) You can run a second Xsession on another virtual console without stopping X Ctrl-Alt-F8 startx -- -bpp 8 :1 and switch between the differetn Xsessions with Ctrl-Alt-F7 and Ctrl-Alt-F8 > Any hints (maybe also to other tree manipulation > software that runs on Linux)? phylo_win njplot Phylodendron c ya -thomas -- Sicheritz Ponten Thomas E. Department of Molecular Biology blippblopp@linux.nu BMC, Uppsala University BMC: +46 18 4714214 BOX 590 S-751 24 UPPSALA Sweden Fax +46 18 557723 http://evolution.bmc.uu.se/~thomas Molecular Tcl: http://evolution.bmc.uu.se/~thomas/tcl Molecular Linux: http://evolution.bmc.uu.se/~thomas/mol_linux De Chelonian Mobile ... The Turtle Moves ... From owner-software@net.bio.net Tue Feb 09 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: treetool for Linux Date: 10 Feb 1999 06:37:30 GMT Organization: Biology, Indiana University - Bloomington Lines: 9 Message-ID: <79r9fa$j3d$1@flotsam.uits.indiana.edu> References: NNTP-Posting-Host: chipmunk.bio.indiana.edu See http://iubio.bio.indiana.edu/treeapp/ for a tree drawing tool, phylodendron, that will work under linux (its done in java). - don -- -- d.gilbert--biocomputing--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu From owner-software@net.bio.net Tue Feb 09 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!remarQ73!supernews.com!remarQ.com!remarQ69!not-for-mail From: Andrew Gardner Newsgroups: bionet.software Subject: Re: DNA sequence analysis for Mac Date: Tue, 09 Feb 1999 20:30:21 -0700 Organization: Posted via RemarQ, http://www.remarQ.com - Discussions start here! Lines: 5 Message-ID: <36C0FD4D.6E682A66@compusmart.ab.ca> References: <36BFB74B.B0D12DC5@compusmart.ab.ca> NNTP-Posting-Host: 207.34.71.125 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: 918617160 OO9TMNNMC477DCF22C usenet87.supernews.com X-Complaints-To: newsabuse@remarQ.com X-Mailer: Mozilla 4.5 [en] (Win95; U) X-Accept-Language: en > As you may know, advertising is really not accepted on this newsgroup, > (and other BIOSCI newsgroups (although plenty do it). Sorry, no harm intended (and that's all I have to say on this subject or any other). From owner-software@net.bio.net Tue Feb 09 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newsfeed.berkeley.edu!newsgate.cuhk.edu.hk!newsgate.netvigator.com!news.netvigator.com!usenet From: "raymond" Newsgroups: bionet.software Subject: ¦³µLoffice 2000 §Ç¸¹§r Date: Wed, 10 Feb 1999 18:47:48 +0800 Organization: Netvigator Lines: 5 Message-ID: <79ro7j$shr$1@imsp009a.netvigator.com> NNTP-Posting-Host: hhttnt03172.netvigator.com X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 ­ü..............¦³office 2000µL§Ç¸¹..µL±o¥Î...³£­øª¾ÂI¦n....... ¦³µLmoney½æ¥¿ª©.....¦pªG¦³¤H¦³office 2000§Ç¸¹...½Ð§Ö D¤ñ§Ú§r............­ø¸Ó From owner-software@net.bio.net Tue Feb 09 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed1.swip.net!swipnet!masternews.telia.net!News.Amsterdam.UnisourceCS!newsfeed.mad.ttd.net!news.bcn.ttd.net!not-for-mail From: "Jose Mª Martinez" Newsgroups: bionet.software Subject: Where can I download Boris Fx 3.5 Date: 10 Feb 1999 22:31:18 GMT Organization: Telefonica Transmision de Datos Lines: 2 Message-ID: <01be5546$74a69b20$31b537c3@default> NNTP-Posting-Host: info1955518149.mundivia.es X-Newsreader: Microsoft Internet News 4.70.1161 Where can I download Boris Fx 3.5 Does anyone have any sites? From owner-software@net.bio.net Tue Feb 09 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!news.net.uni-c.dk!not-for-mail From: "S.W. Rasmussen" Newsgroups: bionet.software Subject: look at Date: Wed, 10 Feb 1999 22:58:43 +0100 Organization: Carlsberg Laboratory Lines: 11 Message-ID: <36C20113.F54028BC@crc.dk> Reply-To: swr@crc.dk NNTP-Posting-Host: 130.226.184.128 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.net.uni-c.dk 918684119 41072 (None) 130.226.184.128 X-Complaints-To: usenet@news.net.uni-c.dk X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en http://web.hku.hk/~xxia/software -- Dr. scient. Søren W. Rasmussen Carlsberg Laboratory, Department of Physiology 10 Gl. Carlsbergvej, DK-2500, Copenhagen, Denmark Phone 45 3327 5230 / 45 3616 2259, Fax 45 3327 4766 E-mail swr@crc.dk, http://www.crc.dk/phys/index.htm From owner-software@net.bio.net Tue Feb 09 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!howland.erols.net!portc02.blue.aol.com!pitt.edu!not-for-mail From: Rich Dudley Newsgroups: bionet.software Subject: Counting tripeptide frequencies Date: Wed, 10 Feb 1999 16:25:46 -0500 Organization: University of Pittsburgh, Dept. of Cell Biology and Physiology Lines: 19 Message-ID: <36C1F959.60962A6E@pitt.edu> Reply-To: rdudley+@pitt.edu NNTP-Posting-Host: whill.cbp.pitt.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en Doe anyone know of a program (WW or Windows) that can enumerate the di- and tri-peptide frequencies in a protein? Ideally, it would contstruct a table at the end of the input and have the sequence and number of occurrences. Thanks! rich -- --- --- --- -- -- -- --- --- --- Richard J. Dudley (rdudley+@pitt.edu) Research Specialist V Dept. of Cell Biology and Physiology University of Pittsburgh http://www.cbp.pitt.edu ---> search BIONET archives at http://www.bio.net <--- From owner-software@net.bio.net Tue Feb 09 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!sunqbc.risq.qc.ca!wesley.videotron.net!Pollux.Teleglobe.net!server-b.cs.interbusiness.it!not-for-mail From: "Roberto Barri" Newsgroups: bionet.software Subject: Home design program Date: Wed, 10 Feb 1999 19:10:14 +0100 Organization: Centro Servizi Interbusiness Lines: 12 Message-ID: <79sh5c$cuo$1@fe2.cs.interbusiness.it> NNTP-Posting-Host: 19