From owner-software@net.bio.net Thu Jul 01 00:36:00 1999 Path: biosci!PRIDNS.SCU.EDU.CN!scunlgbc From: scunlgbc@PRIDNS.SCU.EDU.CN ("afei") Newsgroups: bionet.software Subject: Request for free DNA sequence analysis software Date: 30 Jun 1999 18:36:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <000101bec361$28880740$823373ca@afei.scu.edu.cn> NNTP-Posting-Host: net.bio.net Dear colleagues, I am a PhD student in China.I have sequenced some genes I isolated.But I don't have any analysis software on hand,so I can't analysize the sequences.If someone can give me this kind of software,I will be very appriciate of it. Yours Sincerely, Shen Bin (Please email me shenbin73@263.net) From owner-software@net.bio.net Thu Jul 01 01:09:00 1999 Path: biosci!SUNM.SHCNC.AC.CN!xietao From: xietao@SUNM.SHCNC.AC.CN (xietao) Newsgroups: bionet.software Subject: Re: Request for free DNA sequence analysis software Date: 30 Jun 1999 19:09:11 -0700 Organization: SIBC Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <199907010102.KAA03122@sunm.shcnc.ac.cn> NNTP-Posting-Host: net.bio.net Hi, "afei", in 99-6-30 18:36:00 £º >Dear colleagues, > > I am a PhD student in China.I have sequenced some genes I isolated.But I >don't have any analysis software on hand,so I can't analysize the >sequences.If someone can give me this kind of software,I will be very >appriciate of it. > >Yours Sincerely, >Shen Bin > >(Please email me shenbin73@263.net) Please visit our institute's homepage: http://dna.sibc.ac.cn/bio/index.htm BTW, where are you? Tao, Xie Shang Institute of Biochemistry From owner-software@net.bio.net Thu Jul 01 06:39:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!remarQ73!remarQ60!supernews.com!remarQ.com!ihug.co.nz!not-for-mail From: "Marcel Dinger" Newsgroups: bionet.software Subject: Genamics - SoftwareSeek Date: Thu, 1 Jul 1999 19:27:59 +1200 Organization: Genamics Lines: 33 Message-ID: <930814429.876145@ham.ihug.co.nz> Reply-To: "Marcel Dinger" NNTP-Posting-Host: ham.ihug.co.nz X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Cache-Post-Path: ham.ihug.co.nz!unknown@p89-max7.ham.ihug.co.nz X-Cache: nntpcache 2.3.3 (see http://www.nntpcache.org/) Genamics SoftwareSeek and other molecular resources at http://genamics.com just got better: With over 650 software entries, 360 journal speed links, and 100+ genome project links, you can be assured that you can find what you need, and find it quickly. 1. SoftwareSeek - The largest collection of software tools available for Windows, MS-DOS, Unix, Linux and Macintosh platforms. Entries are classifed into several categories, including DNA sequence analysis, protein structure analysis, RNA structure prediction, molecular modeling, image analysis, and sequence alignment. 2. GenomeSeek - A searchable database of current information about microbial genome projects with links to relevant sites and publications. The database contains over 100 entries. 3. JournalSeek - A searchable index to hundreds of journals, providing easy access to a wealth of information. JournalSeek presently contains more than 360 journals, in a broad range of topics including molecular biology, biochemistry, microbiology, neuroscience, immunology, and cancer. We are committed to keeping the information on our pages as up-to-date as possible and encourage input from our users. We don't require any sort of log-in procedure, and our pages are not loaded with cumbersome advertising banners. Marcel Dinger, Genamics. From owner-software@net.bio.net Thu Jul 01 07:43:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software Subject: Re: Request for free DNA sequence analysis software Date: 01 Jul 1999 09:37:06 +0100 Organization: The Sanger Centre Lines: 25 Message-ID: References: <000101bec361$28880740$823373ca@afei.scu.edu.cn> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 930818209 8583 193.60.84.160 (1 Jul 1999 08:36:49 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 1 Jul 1999 08:36:49 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 scunlgbc@PRIDNS.SCU.EDU.CN ("afei") writes: > I am a PhD student in China.I have sequenced some genes I isolated.But I > don't have any analysis software on hand,so I can't analysize the > sequences.If someone can give me this kind of software,I will be very > appriciate of it. I am developing a free sequence analysis package called EMBOSS (European Molecular Biology Open Software Suite) which runs on all common Unix systems. EMBOSS is a collaboration with members of EMBnet, including the Chinese national node at Peking University. The EMBOSS project web pages are at http://www.sanger.ac.uk/Software/EMBOSS/ There is an alpha release (changing daily) on our FTP server. First beta release is due as soon as the command line sytax is stable. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-software@net.bio.net Thu Jul 01 07:46:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.concentric.net!netnews.com!isdnet!pasteur.fr!ezili.sis.pasteur.fr!bortz From: bortzmeyer@pasteur.fr (Stephane Bortzmeyer) Newsgroups: bionet.software Subject: Re: Request for free DNA sequence analysis software Date: 1 Jul 1999 08:40:54 GMT Organization: Institut Pasteur Lines: 22 Sender: bortz@ezili.sis.pasteur.fr (Stephane Bortzmeyer) Distribution: world Message-ID: <7lf9il$9ml$1@desdemone.pasteur.fr> References: <000101bec361$28880740$823373ca@afei.scu.edu.cn> NNTP-Posting-Host: ezili.sis.pasteur.fr X-Trace: desdemone.pasteur.fr 930818454 9941 157.99.60.56 (1 Jul 1999 08:40:54 GMT) X-Complaints-To: usenet@pasteur.fr NNTP-Posting-Date: 1 Jul 1999 08:40:54 GMT To: scunlgbc@PRIDNS.SCU.EDU.CN,shenbin73@263.net X-Newsreader: xrn 9.01 In article <000101bec361$28880740$823373ca@afei.scu.edu.cn>, scunlgbc@PRIDNS.SCU.EDU.CN ("afei") writes: > I am a PhD student in China.I have sequenced some genes I isolated.But I > don't have any analysis software on hand,so I can't analysize the > sequences. "free" in English is ambiguous. Do you refer to freedom or to price? For "free as in free speech" software, there are several sources, it depends on your platform. For instance, if you use Debian/GNU Linux: http://www.pasteur.fr/units/sis/debian/biology-en.html You'll find Blast, Seaview, and their friends. If you run another brand of Linux: http://evolution.bmc.uu.se/~thomas/mol_linux/ http://www.llp.fu-berlin.de/lsoft/Z/2/ etc. From owner-software@net.bio.net Thu Jul 01 11:10:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!masternews.telia.net!news.algonet.se!newsfeed1.telenordia.se!algonet!newsfeed1.funet.fi!news.helsinki.fi!not-for-mail From: Rasmus Paetau Newsgroups: bionet.software Subject: Free plasmid drawing software for Mac? Date: 1 Jul 1999 14:50:09 +0300 Organization: University of Helsinki Lines: 12 Message-ID: <7lfklh$r8k@vesuri.Helsinki.FI> NNTP-Posting-Host: vesuri.helsinki.fi Is there any good plasmid drawing software that is free for Macintoshes? MacPlasmap and Plasmid artist are giving me trouble... Thanks in advance, Rasmus Paetau (If you reply via email, remove nospam from the address) -- || E-mail: rpaetau@cc.helsinki.fi || University of Helsinki || || WWW: http://www.hut.fi/~rpaetau || Faculty of Medicine || From owner-software@net.bio.net Thu Jul 01 14:48:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!newsswitch.lcs.mit.edu!newsfeed.ecrc.net!newsfeed.nacamar.de!newsfeed.nacamar.de!rz.uni-karlsruhe.de!news.uni-stuttgart.de!news.belwue.de!stremob.pci.chemie.uni-tuebingen.de!user From: merrydoc@yeamob.pci.chemie.uni-tuebingen.de (MerryDoc) Newsgroups: bionet.software Subject: Re: Free plasmid drawing software for Mac? Date: Thu, 01 Jul 1999 17:42:23 +0200 Organization: InterNetNews at News.BelWue.DE (Stuttgart, Germany) Lines: 53 Message-ID: References: <7lfklh$r8k@vesuri.Helsinki.FI> NNTP-Posting-Host: stremob.pci.chemie.uni-tuebingen.de In article <7lfklh$r8k@vesuri.Helsinki.FI>, Rasmus Paetau wrote: > Is there any good plasmid drawing software that is free for Macintoshes? > MacPlasmap and Plasmid artist are giving me trouble... > > Thanks in advance, > Rasmus Paetau Hi Rasmus, I have written a plasmid drawing program for the Macintosh which I have released as Freeware. It allows to draw circular or linear maps. It was originally intended for our lab use, so it is anything but polished. It converts lists of restriction sites and fragment/gene positions into Postscript files. Its weak points in short - It is a Hypercard stack, so you need Hypercard to run it (luckily, speed is no problem, there are no processor intensive steps involved) - The output are Postscript files in Illustrator format. To view and to further edit the picture (which you will have to, see below), you need either Adobe Illustrator, or the Shareware EPStoPICT, which produces a fully editable, object oriented PICT version of the graphics. - The program does not care for overlapping labels, so in most cases you must do some fine-tuning On the other hand, the program - allows "electronic cloning", so you can quickly construct new plasmids from those already entered in the program - can draw all plasmids at the same size, but also using the same (or any you want) scale (that was the primary reason for me to write the program, most commercial programs had (still have?) no way to specify the drawing scale (except by different magnification in the page setup) - draws linear and circular maps, allows borders of various widths and fills of grays, arrows... - Output quality is great, thanks to Postscript - The price is right For a more detailed description, including screen shots of the output graphics, see and that is also the place to download the stack: (BTW, there is also a stack for the organization of plasmid/strain collections available) Kai ----------------------------------------------------------------------- Dr. Kai-Uwe Fröhlich, Physiologisch-chemisches Institut, Hoppe-Seyler-Str. 4, 76072 Tübingen, Germany From owner-software@net.bio.net Thu Jul 01 17:40:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newspeer.monmouth.com!remarQ-easT!supernews.com!remarQ.com!attmtf!attmt1!ip.att.net!news.merck.com!internal.merck.com From: mark_yeager@merck.com (Mark Yeager) Newsgroups: bionet.software Subject: Re: Free plasmid drawing software for Mac? Date: Thu, 01 Jul 1999 14:31:17 -0400 Organization: Merck Research Labs Lines: 16 Message-ID: References: <7lfklh$r8k@vesuri.Helsinki.FI> NNTP-Posting-Host: news.merck.com In article <7lfklh$r8k@vesuri.Helsinki.FI>, Rasmus Paetau wrote: > Is there any good plasmid drawing software that is free for Macintoshes? > MacPlasmap and Plasmid artist are giving me trouble... Try the free Vector NTI viewer: http://informaxinc.com/view/viewer.html Just construct your plasmid as a Genbank formatted text file (see examples) and voila! The contents of this message express only the sender's opinion. This message does not necessarily reflect the policy or views of my employer, Merck & Co., Inc. All responsibility for the statements made in this Usenet posting resides solely and completely with the sender. From owner-software@net.bio.net Thu Jul 01 21:01:00 1999 Path: biosci!BLA-BLA.COM!ashleyf From: ashleyf@BLA-BLA.COM ("Marcus") Newsgroups: bionet.software Subject: Oh, You Didn't Know Date: 1 Jul 1999 15:01:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: <199907012200.PAA11083@net.bio.net> NNTP-Posting-Host: net.bio.net Start your own 1-900 business or Adult Web Site Business! People are making $$$ week, after week in the 1-900 business. We'll teach you all of our incredible secrets that will take your new exciting business to a whole new level! It's The Simplest and Most Exciting Business You Could Ever Start! *You'll use our "state" of the art equipment! *You'll use our "Live 1 on 1 Psychics" & "Chat Line" girls! *You'll use our incredible Date Line program(s)! No chargbacks! Quick payouts! No expertise needed! 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For a free color brochure: reply to: mailto:netopps@bigfoot.com?subject=brochure With the following information: Name:_________________ Address:_________________ City/State/Zip:_________________ email address:_________________ Telephone:_________________ (optional) ///////////////////////////////////////////// To be removed permanantly from this list reply to: mailto:jodyt@canoemail.com?subject=remove ///////////////////////////////////////////// From owner-software@net.bio.net Fri Jul 02 07:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!dispose.news.demon.net!demon!newspeer.monmouth.com!howland.erols.net!spring.edu.tw!feeder.seed.net.tw!news.seed.net.tw!not-for-mail From: lotmail@ms32.url.com.tw Newsgroups: bionet.software Subject: ¤C¤ë¥÷³Ì·s300¸Uµ§¦W³æ Date: 2 Jul 1999 07:54:32 GMT Organization: lotmail Message-ID: <7lhr7o$c2j$2@news.seed.net.tw> NNTP-Posting-Host: cl86-59.dialup.seed.net.tw Lines: 29 ³o¬O¤@«Ê¼s§i«H ­Y³y¦¨§Aªº§xÂZ ½Ð§A¤j¤H¤j¶q ¦h¦h¥]²[........ ºô¸ô¦æ¾Pªº³Ì¨Î¤u¨ã ¤C¤ë¥÷³Ì·s¦W³æ(!!·s¼W155¸Uµ§²Ö¿n¬°300¸Uµ§!!) »Ý­nºCºC´M§ä«È¤á¶Ü?²{¦b§Ú­ÌÀ°±z¦¬¶°¤F300¸Uµ§·s¦a§},¨Cµ§¸ê®Æ«OÃÒ¥¿½T,·Q·Q300¸U«È¤áE-MAIL ¨Ì¾÷²v¨Ó»¡±zªº²£«~°â»ù200¤¸*10¸U=20,000,000³o¼Ë´N¦³¨º»ò¦hªºÀç·~ÃB¦óªp¬O300¸U©O!!!!¥H³Ì¤Öªº ¸êª÷Àò¨ú³Ì¦hªº§Q¼í¤£¬O«Ü´Î¶Ü!!! ²£«~¥]§t: 300¸UE-MAILµ§¸ê®Æ(¯Â¤å¦r®æ¦¡) ¼s§iµo«H±M¥Î³nÅé2®M,¦Û¤v·íMAIL¦øªA¾¹¶W´Î³nÅé¦A¥[¤W¨Ï¥Î¯µÓD±Ð§A¦p¦óµo«H¤£·|³QISP°±Åv!!!! ¦¬¶°NEWS E-MAIL ³nÅé1®M ¥H¤W¥u­n400¤¸¥]§t¶l¶O ÁʶR¤èªk±Ä¶l§½¥N¦¬±b´Ú¤è¦¡³f¨ì±z¤â¤W¦A¥I´Úµ¹¶l®t ©m¦W: ¦a§}: ¹q¸Ü: ÁʶR®M¼Æ: ================================================================= ­qÁÊ«H½c lotmail@ms32.url.com.tw From owner-software@net.bio.net Fri Jul 02 07:01:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!btnet-peer!btnet!newspeer.clara.net!news.clara.net!remarQ-uK!remarQ.com!supernews.com!tank.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!biosci From: pujadas@argo.urv.es (Gerard Pujadas) Newsgroups: bionet.software Subject: DNASTAR ---> FASTA format for Macintosh Date: 2 Jul 1999 08:55:10 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 26 Message-ID: NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Trace: niobium.hgmp.mrc.ac.uk 930902110 24348 193.62.192.80 (2 Jul 1999 07:55:10 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 2 Jul 1999 07:55:10 GMT X-Received: from mserv1.dl.ac.uk (root@mserv1.dl.ac.uk [148.79.160.65]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA13555 for ; Fri, 2 Jul 1999 08:55:07 +0100 (BST) X-Received: from argo.urv.es (argo.urv.es [130.206.36.12]) by mserv1.dl.ac.uk with ESMTP id IAA19337 (8.8.8/5.4[ref postmaster@dl.ac.uk] for dl.ac.uk from pujadas@argo.urv.es); Fri, 2 Jul 1999 08:55:07 +0100 (BST) X-Precedence: first-class X-Received: from [130.206.36.86] (macbi77.urv.es [130.206.36.86]) by argo.urv.es (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA15752 for ; Fri, 2 Jul 1999 09:48:19 +0200 (MDT) X-To: bio-software@dl.ac.uk X-MIME-Autoconverted: from quoted-printable to 8bit by hgmp.mrc.ac.uk id IAA13556 Dear all, I would like to find a Macintosh software that allow to convert more than a hundred of protein sequences files in DNASTAR format into their equivalent FASTA format files. It could be preferred that the application support drag-and-drop use. Thanks in advances for your help. Yours sincerely. Gerard. =========================================================================== DR. GERARD PUJADAS BIOTECNOLOGIA COMPUTACIONAL DEPT. BIOQUIMICA I BIOTECNOLOGIA E-MAIL: pujadas@quimica.urv.es UNIV. ROVIRA I VIRGILI PHONE: 34-977 559565 PLAÇA IMPERIAL TARRACO 1 FAX: 34-977 559597 43005 TARRAGONA (CATALONIA) STATE: SPAIN (EUROPEAN UNION) =========================================================================== --- From owner-software@net.bio.net Fri Jul 02 22:24:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.gtei.net!firehose.mindspring.com!not-for-mail From: john_q_barlow@hotmail.com (John Barlow) Newsgroups: bionet.software Subject: Re: DNASTAR ---> FASTA format for Macintosh Date: 2 Jul 1999 22:31:12 GMT Organization: MindSpring Enterprises Lines: 40 Message-ID: <7ljejg$gc5$1@nntp4.atl.mindspring.net> References: NNTP-Posting-Host: d1.56.3e.bd Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 X-Newsreader: WinVN 0.99.9 (Released Version) (x86 32bit) In article , pujadas@argo.urv.es says... Hi Gerard: I do not know if an application of this kind exists for the Mac, however, if you do not mind transferring files from Mac to PC, you can use SeqVerter for Windows to do exactly this task. It is drag-and-drop and will batch process all the files. SeqVerter is free and can be downloaded from: http://www.genestudio.com. Cheers! John > > > Dear all, > > I would like to find a Macintosh software that allow to convert >more than a hundred of protein sequences files in DNASTAR format into their >equivalent FASTA format files. It could be preferred that the application >support drag-and-drop use. > > Thanks in advances for your help. > > Yours sincerely. > > Gerard. > >=========================================================================== >DR. GERARD PUJADAS >BIOTECNOLOGIA COMPUTACIONAL >DEPT. BIOQUIMICA I BIOTECNOLOGIA E-MAIL: pujadas@quimica.urv.es >UNIV. ROVIRA I VIRGILI PHONE: 34-977 559565 >PLAÇA IMPERIAL TARRACO 1 FAX: 34-977 559597 >43005 TARRAGONA (CATALONIA) >STATE: SPAIN (EUROPEAN UNION) >=========================================================================== > > >--- From owner-software@net.bio.net Sat Jul 03 11:25:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!yellow.newsread.com!netaxs.com!newsread.com!newspeer1.nac.net!news.maxwell.syr.edu!nntp2.deja.com!nnrp1.deja.com!not-for-mail From: mboo@seqnet.dl.ac.uk Newsgroups: bionet.software Subject: Compiling Namot for Linux Date: Sat, 03 Jul 1999 12:09:57 GMT Organization: Deja.com - Share what you know. Learn what you don't. Lines: 15 Message-ID: <7lkuii$5hd$1@nnrp1.deja.com> NNTP-Posting-Host: 193.113.139.190 X-Article-Creation-Date: Sat Jul 03 12:09:57 1999 GMT X-Http-User-Agent: Mozilla/3.04 (WinNT; I) X-Http-Proxy: 1.0 x38.deja.com:80 (Squid/1.1.22) for client 193.113.139.190 Hi I recently obtained Namot from LANL's ftp server. It compiles without problems after adding -L/usr/X11R6/lib (holds the libX11.a file) but It crashes when I sattempt to type text into any dialogue box. I've re-installed the xview and openwin libs and binaries on my system but it hasn't helped. Any clues? Dayo Sent via Deja.com http://www.deja.com/ Share what you know. Learn what you don't. From owner-software@net.bio.net Sat Jul 03 19:50:00 1999 Path: biosci!cnn.nas.nasa.gov!newsfeed.stanford.edu!uchinews2!yellow.newsread.com!netaxs.com!newsread.com!newsfeed.fast.net!uunet!ffx.uu.net!in5.uu.net!news.ici.net!not-for-mail From: "Hilton Evans" Newsgroups: bionet.software Subject: Draw Chemical Structures Date: Sat, 3 Jul 1999 12:25:37 -0400 Organization: ChemPen Software Lines: 8 Message-ID: <7lld6r$p5i$1@bashir.ici.net> Reply-To: "Hilton Evans" NNTP-Posting-Host: d-ma-superpop-2-155.ici.net Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Chempen Chemical Structure Drawing -- http://home.ici.net/~hfevans/chempen.htm ChemPen3D Molecular Mechanics for Win95/NT -- http://home.ici.net/~hfevans/chempen3d.htm -- Hilton Evans Organic Reactions -- http://home.ici.net/~hfevans/reactions.htm Coming Summer 1999 -- NMR Shifts Prediction From owner-software@net.bio.net Sat Jul 03 23:40:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!agate!usenet From: Michael Schmitz Newsgroups: bionet.software Subject: Re: Compiling Namot for Linux Date: Sat, 03 Jul 1999 17:34:41 -0700 Organization: Tinoco Lab, UC Berkekely / Lawrence Berkeley Laboratory Lines: 13 Message-ID: <377EAC21.B907E991@lbl.gov> References: <7lkuii$5hd$1@nnrp1.deja.com> NNTP-Posting-Host: sb19.cchem.berkeley.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX 6.5 IP32) mboo@seqnet.dl.ac.uk wrote: > I recently obtained Namot from LANL's ftp server. It compiles without > problems after adding -L/usr/X11R6/lib (holds the libX11.a file) but It > crashes when I sattempt to type text into any dialogue box. I've > re-installed the xview and openwin libs and binaries on my system but it > hasn't helped. > > Any clues? What versions of libc, libX11 etc. does this happen with? Last time I built it there were no problems, but that's been a while ago... Michael From owner-software@net.bio.net Sun Jul 04 11:12:00 1999 From: "Ò²¨K¥S" Newsgroups: bionet.software Subject: ½Ö¤H¦³Real audio G3 ªº¤U¸üsite©O? ­ø¸Ó«{!! Date: Sat, 3 Jul 1999 19:46:34 +0800 Organization: Hongkong Baptist University Lines: 3 Message-ID: <7lnhck$bg$1@power25t.hkbu.edu.hk> NNTP-Posting-Host: 158.182.23.151 X-Trace: power25t.hkbu.edu.hk 931088596 368 158.182.23.151 (4 Jul 1999 11:43:16 GMT) X-Complaints-To: pm@hkbu.edu.hk NNTP-Posting-Date: 4 Jul 1999 11:43:16 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!uninett.no!newsfeed.nacamar.de!newsfeed.nacamar.de!f.de.uu.net!do.de.uu.net!uunet!ams.uu.net!ffx.uu.net!in5.uu.net!news-hk.telia.net!d2o501.telia.com!newsgate.cuhk.edu.hk!power25t.hkbu.edu.hk!not-for-mail ½Ö¤H¦³Real audio G3 ªº¤U¸üsite©O? ­ø¸Ó«{!! From owner-software@net.bio.net Sun Jul 04 16:32:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!portc02.blue.aol.com!audrey03.news.aol.com!not-for-mail From: ksookoo@aol.com (KSookoo) Newsgroups: bionet.software Subject: RN Exam Softare? Got any? Lines: 2 NNTP-Posting-Host: ladder06.news.aol.com X-Admin: news@aol.com Date: 04 Jul 1999 17:26:42 GMT Organization: AOL http://www.aol.com Message-ID: <19990704132642.23758.00006142@ng-cf1.aol.com> Interested in software for assistance in the Registered Nurse Exam. Can anyone help? From owner-software@net.bio.net Sun Jul 04 19:22:00 1999 Path: biosci!USA.NET!netware33 From: netware33@USA.NET Newsgroups: bionet.software Subject: ADV: Date: 4 Jul 1999 13:22:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: <989.283923.160058.netware33@usa.net> NNTP-Posting-Host: net.bio.net ************************************************** This is a one time mailing, no need to be removed. ************************************************** FLAT RATE LONG DISTANCE IS NOW ACTIVE AND AVAIALBLE FOR U.S. PEOPLE TO USE NOW! MAJOR ANNOUNCEMENT: No matter if you're a business or simply a normal user, you can now have a predictable, flat rate monthly long distance bil and save up to 80% of what you now pay...AND, as an option, you can tell yor friends about this highly desirable service and generate $10,000 a year from home...and now so will you! 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From owner-software@net.bio.net Mon Jul 05 07:24:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!spring.edu.tw!netnews.hinet.net!news From: dreamcast023@ms1.tomail.com.tw Newsgroups: bionet.software Subject: ³Ìªñ±`³QÀb«È¿NÂZ¶Ü?³Ì·s¨¾ªvÀb«È¥úºÐ!! Date: 5 Jul 1999 08:18:34 GMT Organization: dreamcast023 Lines: 187 Message-ID: <7lppoq$6d7@netnews.hinet.net> NNTP-Posting-Host: h21.s151.ts31.hinet.net ³o¬O¤@«Ê¼s§i«H ­Y³y¦¨§Aªº§xÂZ ½Ð§A¤j¤H¤j¶q ¦h¦h¥]²[......... ±Ð±z¦p¦ó¦bºô¸ô¤¤¦Û«Oªº¥úºÐ ¾ã¤ù¥úºÐ ¥u­n400¤¸ §Aª¾¹D¦b§A¤Wºôªº³~¤¤ ¦³¤H¥i¥HµLÁnµL®§ªº¶i¤J©pªº¹q¸£ ÅѨú§A©Ò¦³ªºÁô¨p ¶i¦Ó³y¦¨©pªº²ö¤j·l¥¢¶Ü ¤£­n»{¬°¤£¥i¯à ¦]¬°·í§Þ³N§e²{¦b§A²´«e®É «OÃÒ§A·|¤j¦Y¤@Åå ¦]¬°¤@ª½¥H¨Ó ´N¬O¦³¤H³o¼Ë°µ ±q¤¤Àò±o¤F¤£ªkªº§Q¯q ¥¿©Ò¿× ª¾¤vª¾©¼ ¦Ê¾Ô¦Ê³Ó ¤µ¤Ñ §Ú§â³o¨Ç§Þ³N §Ë¦¨°ê¤º²Ä¤@¤ù¦¬¶°§¹¾ãªºÀb«È¥úºÐ,¤£¦ý±Ð§A«ç»ò¥h¯}¸Ñ, §ó±Ð§A¦p¦ó¥h¨¾½d©ó¥¼µM,³Ì­«­nªº¬O:¥¦¬O¤@¤ù§¹¾ãªº¤¤¤å¤¶­±,¤¤¤å»¡©ú®Ñ, °£«D±z³s¬Ý¦rªº¯à¤O³£¦³§xÃø, §_«h§A¤@©wª¾¹D§Ú¦b»¡¤°»ò!! ¦³¤H°Î¦W¬µ§Aªº«H½c,§A¥iª¾¹D¦p¦ó¨¾ªv¤Î³ø´_??(¥]¬A¬µ§AE-mail³£ºâ¬OÀb«È!) §A¶}ºô¸ô©@°Ø©±,¥iª¾¹DÀb«È³Ì³ßÅwªº´N¬O¤W§Aªº¯¸¥h¸Õ¥\¤O?§A¥iª¾¨äµM¦Ó¨¾¨äµM? §A¥i´¿·Q¹L,§A¥u¬O¤@­Ó¤Wºô¸ôªº¥­¤Z¤H,¥iª¾¹DÀb«È¤]¥i¥h§â§A¤Wºôªº±K½X¤Î¦WºÙ ¨ú¦^¦Û¤v¥Î,Åý§Aªá¿ú¤S·í¤jÀY?¤£¥u¦p¦¹,¥L¤]¥iª½¨ú§A¹q¸£¤ºªº¸ê®Æ,¥]¬A±þÀÉ®× ¤ÎÅý§A·í¾÷?§Aª¾¹D­ì²z,«ç»ò°µ?¦Ó¤S¦p¦ó¨¾¤î©O? §A¦³¥ÎICQªº"¦n"²ßºD¶Ü?¥iª¾ICQ¦w¥þ©Ê¬Æ®tªº²{¦b,§AªºICQ¬OÀb«È³Ì¤jªº·Å§É?¤@ ¼Ë¥i³z¹LICQ¥h°µ¤J«I¤ÎºÞ²zªº°Ê§@,´N¬O§â§AµwºÐ·í¦¨¬O¦Û¤v®a¤@¼Ë,·R®³¤°»ò´N ®³¤°»ò,·íµM¤]¬O¥]¬A§Aªº±K½X¤Î¦WºÙ..... ¦pªG§A¤£´¿Å¥¹L³o¨Ç¨Æ,¨º§A´N¬O³Ì¤jªº°ª¦MÀI¸s,§A¥iª¾¹D¦p¦ó¥h¤F¸Ñ³oºô¸ôªº¶Â ·t­±? ---------------------------------------------------------------------------- 400¤¸©Î³\¥u¬O¤@¹yÀë¥ú±ßÀ\ªº¥N»ù¡A¤]¥i¯à¬O§A¸òªB¤Í¥hKTYªº°ò¥»®ø¶O ¦ý¬O²{¦b«o¯à¶R¨ì§AªºÅv¯q¤Î¤@½ú¤lªº§Þ³N¡A§A¦ó¼Ö¤£¬°©O¡H§Ú¤]¸ò±z°µ «Oµý¡A§A²{¦b¦b¸É¬É¤¤¤]µ´¹ï¬Ý¤£¨ì³o¤@¤ù¥úºÐ¡A¦]¬°¬OÀb«È¦Û¤vªº¦¬Âà ¡A³o¬O²Ä¤@¦¸¬y¥X¥«­±¡A¤é«á©Î³\·|¦³¸É¬É¦¬¿ý¥h½æ¡A¦ý¬O±z¦pªG¤é«á¦A ¥h¶R¡A¸É¬Éª¾¹D³o¤ù¥úºÐªº§Q®`Ãö«Y¡A¤]¸Ó¤£·|§¹¾ã¦¬¿ý¡A·d¤£¦nÁÙ©ñ¤F ¡¨¯S¬¥¥ì¡¨µ{¦¡¶i¥h(Å¥¤£À´¡H´N§â¤@¤ä¤ì°¨µ{¦¡Âæb¨ä¥¦µ{¦¡¤¤AUTORUN ¤]¦æ¡A¥H«á¥u­n§A¤@¤Wºô´Nµ¥©ó§â¦Û¤v°eµ¹¤H®a¡A³Q¹ï¤èµs¥Î±K½X¤Wºô³£ ¤£ª¾¹D......)±z¦Ò¼{¦Ò¼{§a! ¥úºÐ¤º®e============================================================== [·í¾Ô¤õµ²§ô,«°¤¤¤H¥Á¿³°ªªö¯Pªºªï±µ«°¥~ªº¤ì°¨,ÁöµMÁ`¦³¤Ö¼Æªº¤Ï¹ï ,] [«oÁÙ¬OµLªkªý¤î³Q"³Ó§Q"¨R©üÀYªº¤H­Ì,¦b¤@¤ùÅw¼Öªº®ð®§¤¤,¤H­Ì°s«á¶º] [¹¡¤§»Ú,¤ì°¨²×©óÅS¥X³g°ýªº¥»©Ê,±q¤ì°¨¸¡¤¤¥X²{ªº¼Ä¤èºë­^ ,¤@Á|¸ÌÀ³] [¥~¦X,.....±O«°!......] ³o´N¬O¯S¬¥¥ìªº¬G¨Æ,[¤ì°¨±O«°°O]...... ºô¸ô¤W¦s¦bµÛ³\¦hªºÀb«È,¦³©Ò¿×ªº³nÅéÀb«È,¤]¦³¤J«IÀb«È. ¦h¥b¬O¦sµÛ¦nª±ªº¤ßºA,¦ý¬O¤]¦s¦bµÛ¦³¤ß¤H¤h........ ¦]¬°·í§Aª¾¹D¯}¸Ñªº¥Î³~¨ì©³¦³¨º¨Ç¤§«á,§A·|¤£¸T¤ß´H.. §A¥i¯à·|¦Û°Ý:§Ú¬O¤U¤@­Ó¶Ü?ÁÙ¬O¤w¸g³Q¤J«I¦Ó¤£¦Ûª¾..... 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Date: 5 Jul 1999 09:15:17 GMT Organization: Technical University Berlin, Germany Distribution: world Message-ID: <7lpt35$r00$4@mamenchi.zrz.TU-Berlin.DE> NNTP-Posting-Host: dns1.schering.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 1.0b.0 Lines: 5 Did anybody succeed in compiling treetool on a Linux machine? Or does anybody know a Unix or Java tool comparable to Win*s TreeView? Thanks for any help. --- Henrik Seidel From owner-software@net.bio.net Mon Jul 05 09:11:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!easynet-fr!ciril.fr!news.u-strasbg.fr!not-for-mail From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: Compiling treetool for Linux - any success? Date: 5 Jul 1999 11:07:25 GMT Organization: CRC - Universite Louis Pasteur Strasbourg France Lines: 19 Message-ID: <7lq3ld$7fb$1@news.u-strasbg.fr> References: <7lpt35$r00$4@mamenchi.zrz.TU-Berlin.DE> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.u-strasbg.fr 931172845 7659 130.79.79.13 (5 Jul 1999 11:07:25 GMT) X-Complaints-To: usenet@u-strasbg.fr NNTP-Posting-Date: 5 Jul 1999 11:07:25 GMT X-Newsreader: knews 1.0b.0 Mail-Copies-To: never In article <7lpt35$r00$4@mamenchi.zrz.tu-berlin.de>, Henrik Seidel writes: > Did anybody succeed in compiling treetool on a Linux machine? Or does > anybody know a Unix or Java tool comparable to Win*s TreeView? Treetool has 2 problems : Xview libraries and support for 8 bits displays only. You'd better use njplot. njplot can be found as a debian package from : http://www.pasteur.fr/units/sis/debian/biology.html And probably as RPM packages from : http://rpmfind.net/linux/RPM/Applications_Bioinformatics.html François. -- François Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France From owner-software@net.bio.net Mon Jul 05 10:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!dispose.news.demon.net!demon!news-lond.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!oleane!pasteur.fr!ezili.sis.pasteur.fr!bortz From: bortzmeyer@pasteur.fr (Stephane Bortzmeyer) Newsgroups: bionet.software Subject: Re: Compiling treetool for Linux - any success? Date: 5 Jul 1999 10:54:05 GMT Organization: Institut Pasteur Sender: bortz@ezili.sis.pasteur.fr (Stephane Bortzmeyer) Message-ID: <7lq2sd$ouh$1@desdemone.pasteur.fr> References: <7lpt35$r00$4@mamenchi.zrz.TU-Berlin.DE> <7lq3ld$7fb$1@news.u-strasbg.fr> NNTP-Posting-Host: ezili.sis.pasteur.fr X-Trace: desdemone.pasteur.fr 931172045 25553 157.99.60.56 (5 Jul 1999 10:54:05 GMT) X-Complaints-To: usenet@pasteur.fr NNTP-Posting-Date: 5 Jul 1999 10:54:05 GMT To: jeanmougin@igbmc.u-strasbg.fr,Henrik Seidel X-Newsreader: xrn 9.01 Lines: 24 In article <7lq3ld$7fb$1@news.u-strasbg.fr>, pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) writes: > Treetool has 2 problems : Xview libraries and support for > 8 bits displays only. Yes, they are problems, but they have solutions. Treetool runs fine on my Linux box with 16-bits display. > You'd better use njplot. njplot can be found as > a debian package from : > > http://www.pasteur.fr/units/sis/debian/biology.html The Debian package of treetool is at the same place :-) > And probably as RPM packages from : > > http://rpmfind.net/linux/RPM/Applications_Bioinformatics.html No. The above is really poor (they just have Blast), probably because serious work is one on Debian only :-) From owner-software@net.bio.net Mon Jul 05 12:33:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!dispose.news.demon.net!demon!newsfeed.nacamar.de!newsfeed.nacamar.de!fu-berlin.de!zrz.TU-Berlin.DE!not-for-mail From: Henrik Seidel Newsgroups: bionet.software Subject: Re: Compiling treetool for Linux - any success? Date: 5 Jul 1999 13:27:12 GMT Organization: Technical University Berlin, Germany Distribution: world Message-ID: <7lqbrg$etn$1@mamenchi.zrz.TU-Berlin.DE> References: <7lpt35$r00$4@mamenchi.zrz.TU-Berlin.DE> <7lq3ld$7fb$1@news.u-strasbg.fr> <7lq2sd$ouh$1@desdemone.pasteur.fr> NNTP-Posting-Host: dns1.schering.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 1.0b.0 Lines: 17 In article <7lq2sd$ouh$1@desdemone.pasteur.fr>, bortzmeyer@pasteur.fr (Stephane Bortzmeyer) writes: >> And probably as RPM packages from : >> >> http://rpmfind.net/linux/RPM/Applications_Bioinformatics.html > > No. The above is really poor (they just have Blast), probably because > serious work is one on Debian only :-) I don't want to comment on that, but I prepared RPMs based on Stephane's Debian package. They can be found at http://www.snafu.de/~henrik.seidel/ Thanks for your help. --- Henrik Seidel From owner-software@net.bio.net Mon Jul 05 12:48:00 1999 Path: biosci!SIRIUS.GAZI.EDU.TR!alevd From: alevd@SIRIUS.GAZI.EDU.TR ("Ars.Alev DOGAN") Newsgroups: bionet.software Subject: superquad Date: 5 Jul 1999 06:48:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Sir, I am a Ph.D. student and a researc assistant in chemistry Department of Gazi Universitiy,Ankara-Turkey.I am interested in potentiometric measurements of some amino acids.I want to get more detailed about the program SUPERQUAD, appreciate if you can help me to buy a copy of it. Thank you in advance for your kind attention. Sincerely yours, Alev Dogan e-mail:alevd@sirius.gazi.edu.tr From owner-software@net.bio.net Mon Jul 05 16:57:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Compiling treetool for Linux - any success? Date: 5 Jul 1999 17:51:09 GMT Organization: Biology, Indiana University - Bloomington Lines: 10 Message-ID: <7lqrad$i3a$1@flotsam.uits.indiana.edu> References: <7lpt35$r00$4@mamenchi.zrz.TU-Berlin.DE> NNTP-Posting-Host: chipmunk.bio.indiana.edu You may want to look at Phylodendron (a tool for phylogenetic tree drawing written in Java). See http://iubio.bio.indiana.edu/treeapp/ and http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/ - Don -- -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu From owner-software@net.bio.net Tue Jul 06 03:10:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!nntp.flash.net!news.flash.net!not-for-mail Message-ID: <37818115.DE9AC611@workingobjects.com> From: Wayne Parrott Organization: WorkingObjects.com X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software Subject: [ANN]PharmTools for Blast and BlastXML Report Processing Available Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 20 Date: Tue, 06 Jul 1999 04:03:28 GMT NNTP-Posting-Host: 209.30.135.138 X-Complaints-To: abuse@flash.net X-Trace: news.flash.net 931233808 209.30.135.138 (Mon, 05 Jul 1999 23:03:28 CDT) NNTP-Posting-Date: Mon, 05 Jul 1999 23:03:28 CDT PharmTools SDK Suite(TM) (Version 1.0) Announcing the free availability of PharmTools SDK Suite(TM) Version 1.0 from WorkingObjects.com. PharmTools SDK is a collection of reusable Java frameworks and toolkits for use in the development of bioinformatics applications. This release includes: the Blast Parsing Framework and BlastXML-SDK. The Blast Parsing Framework is a set of design patterns and Java classes for processing native (i.e., local) and NCBI website generated Blast reports. BlastXML-SDK extends the Blast Parsing Framework functionality to support the creation and processing of BlastXML documents. This release includes documentation, a license that allows it to be freely employed within other products, source code, and examples. The PharmTools SDK Suite may be downloaded from the WorkingObjects.com website at http://www.workingobjects.com. Wayne Parrott WorkingObjects.com From owner-software@net.bio.net Tue Jul 06 05:30:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!easynet-fr!ciril.fr!news.u-strasbg.fr!not-for-mail From: Julie THOMPSON Newsgroups: bionet.software Subject: Clustal W, Clustal X version 1.8 Date: Tue, 06 Jul 1999 08:26:32 +0200 Organization: IGBMC Lines: 72 Message-ID: <3781A197.45D79C68@titus.u-strasbg.fr> NNTP-Posting-Host: alibaba.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.u-strasbg.fr 931245997 4084 130.79.79.210 (6 Jul 1999 07:26:37 GMT) X-Complaints-To: usenet@u-strasbg.fr NNTP-Posting-Date: 6 Jul 1999 07:26:37 GMT X-Mailer: Mozilla 4.5 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Clustal W, Clustal X (Version 1.8) Release Announcing a release of upgrades to the freely available Clustal W and X multiple sequence alignment programs. Clustal X provides a windows interface (using the NCBI Vibrant toolkit) to Clustal W. With this release, Clustal X is at last no longer beta test and we can bring the version numbers of Clustal X into line with Clustal W. Note the version 1.8 programs share the same algorithms and parameterisation and produce exactly the same alignments. The main changes to Clustal W are reparameterisation of the alignment algorithm and a number of bug fixes (listed in the README). The Gonnet PAM series is now the default protein matrix series and gap extension penalty has been increased. Clustal X has in addition received a lot of work to the windows interface. Users should note that screen refresh is quite slow on all compilations of Clustal X. In addition the Mac and PC platforms suffer from a double refresh during window resizing. These limitations, though annoying, do not seriously affect the utility of the program. Clustal W and versions of Clustal X for PowerMac, PC (32 bit), and UNIX (Linux, Alpha, SGI, Sun) can be downloaded from several websites including: IGBMC ftp://ftp-igbmc.u-strasbg.fr/pub/ EBI ftp://ftp.ebi.ac.uk/pub/software/ and all sites with mirrors to the EBI Problems with the 1.8 release may be reported to any of the authors, including: Julie Thompson (julie@igbmc.u-strasbg.fr) Toby Gibson (Toby.Gibson@EMBL-Heidelberg.de) Des Higgins (des@chah.ucc.ie) Francois Jeanmougin (pingouin@igbmc.u-strasbg.fr) especially for LINUX... ****************************************************************************** POLICY ON COMMERCIAL DISTRIBUTION OF CLUSTAL W/X Clustal W/X is freely available to the user community. However, Clustal W/X is increasingly being distributed as part of commercial sequence analysis packages. To help us safeguard future maintenance and development, commercial distributors of Clustal W/X must take out a NON-EXCLUSIVE LICENCE. Anyone wishing to commercially distribute version 1.8 of Clustal W/X should contact the authors unless they have previously taken out a licence. ****************************************************************************** From owner-software@net.bio.net Tue Jul 06 05:30:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!easynet-fr!ciril.fr!news.u-strasbg.fr!not-for-mail From: Julie THOMPSON Newsgroups: bionet.software Subject: Re: Compiling treetool for Linux - any success? Date: Tue, 06 Jul 1999 08:24:47 +0200 Organization: IGBMC Lines: 13 Message-ID: <3781A12F.3A661273@titus.u-strasbg.fr> References: <7lpt35$r00$4@mamenchi.zrz.TU-Berlin.DE> NNTP-Posting-Host: alibaba.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.u-strasbg.fr 931245893 4084 130.79.79.210 (6 Jul 1999 07:24:53 GMT) X-Complaints-To: usenet@u-strasbg.fr NNTP-Posting-Date: 6 Jul 1999 07:24:53 GMT X-Mailer: Mozilla 4.5 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Henrik Seidel wrote: > Did anybody succeed in compiling treetool on a Linux machine? Or does > anybody know a Unix or Java tool comparable to Win*s TreeView? > > Thanks for any help. > --- Henrik Seidel Have you tried NJPLOT from Manolo Guoy (mgouy@biomserv.univ-lyon1.fr). A linux executable is available. Julie Thompson From owner-software@net.bio.net Tue Jul 06 11:22:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!ctu-gate!news.nctu.edu.tw!news.neto.net!hp1.timenet.net!netnews.hinet.net!news From: dreamcast023@ms1.tomail.com.tw Newsgroups: bionet.software Subject: ³Ì·s¨¾ªvÀb«È¥úºÐ!! Date: Mon, 5 Jul 1999 17:59:32 +0800 Organization: DCI HiNet Lines: 229 Message-ID: <931197572@wowo> Reply-To: dreamcast023@ms1.tomail.com.tw NNTP-Posting-Host: h119.s147.ts31.hinet.net Content-Type: text/plain; charset=us-ascii ³o¬O¤@«Ê¼s§i«H ­Y³y¦¨§Aªº§xÂZ ½Ð§A¤j¤H¤j¶q ¦h¦h¥]²[......... ±Ð±z¦p¦ó¦bºô¸ô¤¤¦Û«Oªº¥úºÐ ¾ã¤ù¥úºÐ ¥u­n400¤¸ §Aª¾¹D¦b§A¤Wºôªº³~¤¤ ¦³¤H¥i¥HµLÁnµL®§ªº¶i¤J©pªº¹q¸£ ÅѨú§A©Ò¦³ªºÁô¨p ¶i¦Ó³y¦¨©pªº²ö¤j·l¥¢¶Ü ¤£­n»{¬°¤£¥i¯à ¦]¬°·í§Þ³N§e²{¦b§A²´«e®É «OÃÒ§A·|¤j¦Y¤@Åå ¦]¬°¤@ª½¥H¨Ó ´N¬O¦³¤H³o¼Ë°µ ±q¤¤Àò±o¤F¤£ªkªº§Q¯q ¥¿©Ò¿× ª¾¤vª¾©¼ ¦Ê¾Ô¦Ê³Ó ¤µ¤Ñ §Ú§â³o¨Ç§Þ³N §Ë¦¨°ê¤º²Ä¤@¤ù¦¬¶°§¹¾ãªºÀb«È¥úºÐ,¤£¦ý±Ð§A«ç»ò¥h¯}¸Ñ, §ó±Ð§A¦p¦ó¥h¨¾½d©ó¥¼µM,³Ì­«­nªº¬O:¥¦¬O¤@¤ù§¹¾ãªº¤¤¤å¤¶­±,¤¤¤å »¡©ú®Ñ, °£«D±z³s¬Ý¦rªº¯à¤O³£¦³§xÃø, §_«h§A¤@©wª¾¹D§Ú¦b»¡¤°»ò!! ¦³¤H°Î¦W¬µ§Aªº«H½c,§A¥iª¾¹D¦p¦ó¨¾ªv¤Î³ø´_??(¥]¬A¬µ§AE-mail³£ ºâ¬OÀb«È!) §A¶}ºô¸ô©@°Ø©±,¥iª¾¹DÀb«È³Ì³ßÅwªº´N¬O¤W§Aªº¯¸¥h¸Õ¥\¤O?§A¥iª¾ ¨äµM¦Ó¨¾¨äµM? §A¥i´¿·Q¹L,§A¥u¬O¤@­Ó¤Wºô¸ôªº¥­¤Z¤H,¥iª¾¹DÀb«È¤]¥i¥h§â§A¤Wºô ªº±K½X¤Î¦WºÙ ¨ú¦^¦Û¤v¥Î,Åý§Aªá¿ú¤S·í¤jÀY?¤£¥u¦p¦¹,¥L¤]¥iª½¨ú§A¹q¸£¤ºªº¸ê ®Æ,¥]¬A±þÀÉ®× ¤ÎÅý§A·í¾÷?§Aª¾¹D­ì²z,«ç»ò°µ?¦Ó¤S¦p¦ó¨¾¤î©O? §A¦³¥ÎICQªº"¦n"²ßºD¶Ü?¥iª¾ICQ¦w¥þ©Ê¬Æ®tªº²{¦b,§AªºICQ¬OÀb«È ³Ì¤jªº·Å§É?¤@ ¼Ë¥i³z¹LICQ¥h°µ¤J«I¤ÎºÞ²zªº°Ê§@,´N¬O§â§AµwºÐ·í¦¨¬O¦Û¤v®a¤@¼Ë ,·R®³¤°»ò´N ®³¤°»ò,·íµM¤]¬O¥]¬A§Aªº±K½X¤Î¦WºÙ..... ¦pªG§A¤£´¿Å¥¹L³o¨Ç¨Æ,¨º§A´N¬O³Ì¤jªº°ª¦MÀI¸s,§A¥iª¾¹D¦p¦ó¥h¤F ¸Ñ³oºô¸ôªº¶Â ·t­±? ---------------------------------------------------------------------------- 400¤¸©Î³\¥u¬O¤@¹yÀë¥ú±ßÀ\ªº¥N»ù¡A¤]¥i¯à¬O§A¸òªB¤Í¥hKTYªº°ò ¥»®ø¶O ¦ý¬O²{¦b«o¯à¶R¨ì§AªºÅv¯q¤Î¤@½ú¤lªº§Þ³N¡A§A¦ó¼Ö¤£¬°©O¡H§Ú¤] ¸ò±z°µ «Oµý¡A§A²{¦b¦b¸É¬É¤¤¤]µ´¹ï¬Ý¤£¨ì³o¤@¤ù¥úºÐ¡A¦]¬°¬OÀb«È¦Û¤v ªº¦¬Âà ¡A³o¬O²Ä¤@¦¸¬y¥X¥«­±¡A¤é«á©Î³\·|¦³¸É¬É¦¬¿ý¥h½æ¡A¦ý¬O±z¦pªG ¤é«á¦A ¥h¶R¡A¸É¬Éª¾¹D³o¤ù¥úºÐªº§Q®`Ãö«Y¡A¤]¸Ó¤£·|§¹¾ã¦¬¿ý¡A·d¤£¦n ÁÙ©ñ¤F ¡¨¯S¬¥¥ì¡¨µ{¦¡¶i¥h(Å¥¤£À´¡H´N§â¤@¤ä¤ì°¨µ{¦¡Âæb¨ä¥¦µ{¦¡¤¤ AUTORUN ¤]¦æ¡A¥H«á¥u­n§A¤@¤Wºô´Nµ¥©ó§â¦Û¤v°eµ¹¤H®a¡A³Q¹ï¤èµs¥Î±K½X ¤Wºô³£ ¤£ª¾¹D......)±z¦Ò¼{¦Ò¼{§a! ¥úºÐ¤º®e =========================================================== === [·í¾Ô¤õµ²§ô,«°¤¤¤H¥Á¿³°ªªö¯Pªºªï±µ«°¥~ªº¤ì°¨,ÁöµMÁ`¦³¤Ö¼Æªº¤Ï ¹ï ,] [«oÁÙ¬OµLªkªý¤î³Q"³Ó§Q"¨R©üÀYªº¤H­Ì,¦b¤@¤ùÅw¼Öªº®ð®§¤¤,¤H­Ì°s «á¶º] [¹¡¤§»Ú,¤ì°¨²×©óÅS¥X³g°ýªº¥»©Ê,±q¤ì°¨¸¡¤¤¥X²{ªº¼Ä¤èºë­^ ,¤@Á| ¸ÌÀ³] [¥~¦X,.....±O«°!......] ³o´N¬O¯S¬¥¥ìªº¬G¨Æ,[¤ì°¨±O«°°O]...... ºô¸ô¤W¦s¦bµÛ³\¦hªºÀb«È,¦³©Ò¿×ªº³nÅéÀb«È,¤]¦³¤J«IÀb«È. ¦h¥b¬O¦sµÛ¦nª±ªº¤ßºA,¦ý¬O¤]¦s¦bµÛ¦³¤ß¤H¤h........ ¦]¬°·í§Aª¾¹D¯}¸Ñªº¥Î³~¨ì©³¦³¨º¨Ç¤§«á,§A·|¤£¸T¤ß´H.. §A¥i¯à·|¦Û°Ý:§Ú¬O¤U¤@­Ó¶Ü?ÁÙ¬O¤w¸g³Q¤J«I¦Ó¤£¦Ûª¾..... 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Particular areas of interest are protein structure prediction, protein fold recognition (threading), and sequence analysis of genomic sequences (in particular transmembrane protein sequences.) The available Studentship is MRC funded and so attracts a significantly higher stipend than most Studentships (7,000-10,000 pounds / year). Ideal candidates should have a knowledge of biology and good computational or mathematical skills. Physics or computer science graduates wishing to apply their skills to biological problems would also be suitable. Details of the research interests in the laboratory can be read from the following WWW page: http://globin.bio.warwick.ac.uk Enquiries about these Studentships should be addressed directly to Dr Jones at the address shown below. Note that normal eligibility requirements for MRC studentships apply, so foreign nationals are not eligible, and candidates would need a 1st or Upper Second class degree (or equivalent). >---------------------------------------------------------------------------< Address: Dept. of Biological | Email: jones@globin.bio.warwick.ac.uk Sciences, University of Warwick, | Tel: +44 1203 523729 Coventry CV4 7AL, U.K. | Fax: +44 1203 523701 From owner-software@net.bio.net Tue Jul 06 15:18:00 1999 Path: biosci!newshost.lanl.gov!not-for-mail From: Carla Kuiken Newsgroups: bionet.software,bionet.jobs Subject: Job opening at HIV Database in Los Alamos Date: Tue, 06 Jul 1999 10:12:37 -0600 Organization: Los Alamos National Laboratory Lines: 32 Message-ID: <37822AF5.3683@lanl.gov> NNTP-Posting-Host: intron.lanl.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: newshost.lanl.gov 931277559 11634 128.165.24.153 (6 Jul 1999 16:12:39 GMT) X-Complaints-To: usenet@lanl.gov NNTP-Posting-Date: 6 Jul 1999 16:12:39 GMT Cc: btk, btf X-Mailer: Mozilla 3.01 (X11; U; SunOS 5.5.1 sun4m) We have a job opening for a Graduate Research Assistant with a background in biology or immunology. The job entails assisting the staff and postdocs doing sequence analyses using existing and new methods, helping maintain and expand the website, literature searches, annotating the sequence database, and assisting in the production of the two yearly Compendia (HIV Sequences and Immunology). Depending on the skills of the GRA, scripting and programming (Perl, C/C++, javascript) can become part of the tasks as well. There are some possibilities for computer training on the job. We are looking for someone with a background in biology or immunology who is able to work independently on challenging data analysis as well as data annotation and routine sequence alignments. A background in sequence analysis or genetics is helpful, but not required. Some computer experience is necessary, preferably on a UNIX platform. Programming skills would be an asset. The HIV Database and Analysis Group has ongoing collaborations with major HIV research groups worldwide. There is a lot of room to expand new ideas and initiatives and to develop new skills. The salary is excellent, and the living environment is one of the best in the country. The GRA program is designed for people who have a bachelors degree or a masters degree, and want ultimately to go on with further graduate studies. GRAs are hired for a period of one year, after which they have to enroll into a graduate program in order to be allowed to continue working as a GRA. The nearby University of New Mexico offers a fairly large selection of graduate programs. For more information or to apply, please send an email to Carla Kuiken (kuiken@lanl.gov). http://hiv-web.lanl.gov From owner-software@net.bio.net Tue Jul 06 18:16:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!newsswitch.lcs.mit.edu!newsfeed.enteract.com!news.maxwell.syr.edu!newsfeed.nacamar.de!fu-berlin.de!news.icm.edu.pl!not-for-mail From: Piotr Kozbial Newsgroups: bionet.software Subject: Database integration with sequence analysis software - how? Date: Tue, 06 Jul 1999 21:14:00 +0200 Organization: http://news.icm.edu.pl/ Lines: 31 Message-ID: <37825578.A352B0CC@ibb.waw.pl> Reply-To: piotrk@ibb.waw.pl NNTP-Posting-Host: pc244.ibb.waw.pl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: sunsite.icm.edu.pl 931288208 7182 148.81.193.76 (6 Jul 1999 19:10:08 GMT) X-Complaints-To: abuse@news.icm.edu.pl NNTP-Posting-Date: 6 Jul 1999 19:10:08 GMT X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.5 i586) X-Accept-Language: en I am interested in testing several ideas about organization of genomic information. Could you please send me references about: 1. Sequences management in relational databases. Databases, I know, store data in tables and rows, but sequences seems to be stored in flat files (i.e. in FASTA format). Is it good idea to chop the sequences and transfer them into relational database? Some kinds of sequences are well suited for storage in relational database (i.e. protein and cDNA sequences), but genomic sequences are not. Is it good idea to cut genomic sequences into fragments containing ORFs with theirs upstream and downstream sequence, and with some positioning information (i.e.. IDs of upstream and downstream ORFs). With each ORF in the database it is possible to store additional information (computed or taken from known literature) like: -cDNA sequence, -IDs of known aa motives, -ID of known conserved structural domains, -ID of interacting proteins, -pre computed information about structural, sequence, and functional homologies (similar to "neighbors" in NCBI databases), -all other information (especially raw experimental data), 2. There are lots of tools for sequence analysis written in perl, c, c++, etc. How the interface between the database and the tools should be designed? Are there any examples? TIA Piotr From owner-software@net.bio.net Wed Jul 07 00:42:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!209.50.235.254!europa.netcrusader.net!204.127.161.3!wn3feed!worldnet.att.net!wnmaster2!not-for-mail From: "Ron Robinson II" Newsgroups: bionet.software Subject: Help! looking for software Date: Tue, 6 Jul 1999 06:39:18 -0700 Organization: AT&T WorldNet Services Lines: 6 Message-ID: <7luauc$mrp$1@bgtnsc02.worldnet.att.net> NNTP-Posting-Host: 12.73.101.164 X-Trace: bgtnsc02.worldnet.att.net 931311372 23417 12.73.101.164 (7 Jul 1999 01:36:12 GMT) X-Complaints-To: abuse@worldnet.att.net NNTP-Posting-Date: 7 Jul 1999 01:36:12 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 I am looking for (and don't laugh) a copy of DOS 3.0 Plus ? if anyone could help, possibly e-mail me a copy, it would be appreciated. A freind still uses it and lost some files. Thanks.... From owner-software@net.bio.net Wed Jul 07 06:52:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!biosci From: ajenkins@nibsc.ac.uk (Adrian Jenkins) Newsgroups: bionet.software Subject: Re: ACCESS NEEDED!!! Date: 7 Jul 1999 08:45:45 +0100 Organization: NIBSC Lines: 52 Message-ID: <3783058F.6298DD29@nibsc.ac.uk> References: <37823C40.5E5D12F@email.com> NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 931333545 25177 193.62.192.80 (7 Jul 1999 07:45:45 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 7 Jul 1999 07:45:45 GMT X-Received: from comsig.nibsc.ac.uk (comsig.nibsc.ac.uk [193.62.43.13]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA17898 for ; Wed, 7 Jul 1999 08:45:41 +0100 (BST) X-Received: from nibsc.ac.uk (cqaiaj.nibsc.ac.uk [193.62.42.49]) by comsig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id IAA21152; Wed, 7 Jul 1999 08:45:26 +0100 (BST) X-Reply-To: ajenkins@nibsc.ac.uk X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en X-To: "Sten A. Hankewitz" X-CC: bio-software@hgmp.mrc.ac.uk Hi there to you. I have recently bought a lap top together with my girlfriend We too would like to have access, Word, Excel etc. The only source of the software is the local Microsoft dealer. So, please take your credit card and purchase it. "Sten A. Hankewitz" wrote: > > Hi! > > I desperately need Microsoft Access 97 or 95 or actually whatever. Can > someone PLEASE tell me the URL I can find it in or maybe some good > person will send it to me by mail. > > I really need it!!! > > Thank you! > > Sten > stenah@email.com -- Enjoy.... Adrian %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL Adrian Jenkins Molecular Virology Group Division of Retrovirology e-mail ajenkins@nibsc.ac.uk http://www.nibsc.ac.uk/ "No plan survives contact with the enemy" von Moltke "To Errr is human, but when the eraser wears out ahead of the pencil; you're overdoing it." Anon %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --- From owner-software@net.bio.net Wed Jul 07 07:25:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!dispose.news.demon.net!demon!ayres.ftech.net!news.ftech.net!bignews.mediaways.net!f.de.uu.net!do.de.uu.net!uunet!ams.uu.net!iafrica.com!news.adamastor.ac.za!not-for-mail From: Gian van der Spuy Newsgroups: bionet.software Subject: How to run xview Date: Wed, 07 Jul 1999 10:19:03 +0200 Organization: Adamastor Message-ID: <37830D77.323B1FD@gerga.sun.ac.za> NNTP-Posting-Host: molbio.biochem.sun.ac.za Mime-Version: 1.0 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.61 [en] (Win98; U) X-Accept-Language: en Lines: 13 Based on advice from this group I have downloaded and compiled namot. I have also installed the xview libraries and binaries. I am quite new to Linux so pardon me if this is a silly question, but how do I now run xview and get namot running in it.

--
Gian van der Spuy
Molecular and Cellular Biology
University of Stellenbosch
South Africa
  From owner-software@net.bio.net Wed Jul 07 18:33:00 1999 Path: biosci!COMPUTER.ORG!fvega From: fvega@COMPUTER.ORG ("Francisco M. De La Vega") Newsgroups: bionet.software Subject: DEADLINE SOON: SNP Data analysis & Mgmnt @ PSB'2000 Date: 7 Jul 1999 12:33:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 127 Sender: daemon@net.bio.net Distribution: world Message-ID: <3783A867.87B94553@computer.org> NNTP-Posting-Host: net.bio.net Dear Colleague, Please note that the deadline for paper submissions to the "Analysis, Management and Application of SNP Data" is due on July 12, 1999. Additional information is attached. I encourage you to submitt a contribution on that date; however let me know if you are interested in submitting, but have difficulty meeting this deadline. Sincerely, Francisco M. De La Vega PE Biosystems ================================================== Human Genome Variation: Analysis, Management and Application of SNP Data A session of the Pacific Symposium on Biocomputing 2000, Honolulu, Hawaii, January 5-9, 2000 Recently there has been considerable interest in using single nucleotide polymorphisms (SNP) for the understanding of complex diseases and for pharamacogenetics. The human genetics community, both private and academic, is engaged in large scale SNP discovery efforts and assay development. With the imminent development of high throughput methodologies for automating the SNP discovery and screening process, it is likely that many if not all of the common polymorphisms will be identified and characterized in the next several years. As is often the case, data production may outpace current data management and analysis capabilities. New, specialized SNP databases are being designed and implemented to capture the impending flood of polymorphism data. Comprehensiveness of the captured data and the exploration of its intellectual content is essential. Computational methods and tools to handle and analyze polymorphism data flow will certainly play an important role in this challenge. Call for Participation The PSB 2000 session "Human Genome Variation: Analysis, Management and Application of SNP Data" aims to provide a timely forum in this area, bringing together computer scientists, bioinformatics specialists and biologists, from academia and industry, to address the forthcoming problems in the utilization of SNP information. We encourage academic, industrial and government scientists to submit manuscripts. In addition to a session for oral presentation of novel peer-reviewed contributions, there will be a panel discussion devised to foster exchange between industry and academic scientists. Participants are invited to discuss their issues with other peers in this panel session. Posters and computer demonstrations are also requested to complement the session. Topics The contributions should pose and discuss a specific problem that the biocomputing community will need to address, describe models, or propose specific solutions to a problem. Sequence polymorphisms will be the common theme, but the computational or theoretical contributions can span areas ranging from population genetics and evolution to data visualization and management. Among the anticipated topics are: Automation of large scale SNP genotyping. Data management and integration for SNP genotyping systems. Evolutionary aspects of genome variability and SNP analysis. Ontologies for human genome variation. SNP database mining and knowledge discovery. Statistical methods for SNP analysis. Tools for high throughput SNP discovery and screening. Visualization and analysis of SNP data. Submissions PSB will publish accepted full papers in an archival proceedings indexed in MEDLINE. All contributed papers will be rigorously peer-reviewed by at least three referees. A limited number of papers will be selected for a 30-minute oral presentation to the full assembled conference. Accepted poster abstracts will be distributed at the conference separately from the archival Proceedings. Please prepare your submission according to the instructions found at the Web page: http://www.cgl.ucsf.edu/psb/cfp-snp.html Dates & Deadlines Paper submissions due: July 12, 1999 Notification of paper acceptance: August 27, 1999 Camera ready of accepted papers due: September 24, 1999 Abstract deadline: October 1, 1999 Meeting: January 5-9, 2000 Conference Information The Pacific Symposium on Biocomputing (PSB 2000) is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. PSB 2000 will be held January 5- 9, 2000, in Honolulu, Hawaii at the Sheraton Waikiki. For more information see the official PSB 2000 Web page at : http://www.cgl.ucsf.edu/psb/ Session Chairs Francisco M. De La Vega, Synthesis and Arrays R&D, PE Biosystems, Foster City, CA, USA. E-mail: DelaveFM@pebio.com Martin Kreitman, Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA. E-mail: mkre@midway.uchicago.edu From owner-software@net.bio.net Wed Jul 07 20:11:00 1999 Path: biosci!daresbury!uninett.no!Norway.EU.net!uio.no!news.netg.se!news-peer-europe.sprintlink.net!news.sprintlink.net!howland.erols.net!nntp.abs.net!newshub2.home.com!news.home.com!news2.rdc1.on.home.com.POSTED!not-for-mail From: "StannyP" Newsgroups: alt.comp.software.financial.peachtree,alt.fan.dean-stark.software.tester,alt.geo-software,alt.med.software,alt.video.dvd.software,bionet.software,bionet.software.acedb,bionet.software.gcg Subject: Top Quality Software Testing Services by Software Testing Lab Inc. for FREE!!! Lines: 42 Organization: TranceSundayProject X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Message-ID: <7ePg3.16670$_A4.369691@news2.rdc1.on.home.com> Date: Wed, 07 Jul 1999 21:00:51 GMT NNTP-Posting-Host: 24.114.37.51 X-Complaints-To: abuse@home.net X-Trace: news2.rdc1.on.home.com 931381251 24.114.37.51 (Wed, 07 Jul 1999 14:00:51 PDT) NNTP-Posting-Date: Wed, 07 Jul 1999 14:00:51 PDT Xref: biosci bionet.software:23792 bionet.software.acedb:2454 bionet.software.gcg:3615 Top Quality Software Testing Services by Software Testing Lab Inc. for FREE!!! As a result of 20 years of research and software engineering experience we have developed a new testing methodology. Our approach allows us to perform Software Quality Assurance and Testing with maximal possible coverage in minimal possible time. Before implementing our methodology into a commercial product we would like to test it ourselves in real-life business situation. We are currently offering a number of Software Quality Assurance and Testing absolutely for free. These services include: - Functional and Structural Unit Testing - Unit, Integration, and System Testing of Software Applications - Client / Server and Internet Applications testing - Load testing - Documentation Testing - Regression Testing - Security Testing - Automated Testing Tools Evaluation (ATTENTION DVELOPERS!!!) ATTENTION AUTOMATED SOFTWARE TESTING TOOLS DEVELOPERS! ATTENTION SOFTWARE DEVELOPMENT COMPANIES! We can make your product better by finding its weaknesses. We can help you to keep your customers satisfied providing a fully tested software product. Now we do it for free! For information contact: Software Testing Lab Inc. 398 Steels Ave. West, Suite 205 Toronto, Ontario L4J 6X3, CANADA E-mail: softtest@istar.ca http:\\www.softtestlab.com From owner-software@net.bio.net Thu Jul 08 00:24:00 1999 Path: biosci!sanger.ac.uk!solovyev From: solovyev@sanger.ac.uk ("Victor Solovyev") Newsgroups: bionet.software Subject: Genes_in_Pictures (Human/Drosophila) Date: 7 Jul 1999 18:24:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 104 Sender: daemon@net.bio.net Distribution: world Message-ID: <9907080218.ZM28768@octane> NNTP-Posting-Host: net.bio.net ============================================================== Genes_in_Pictures (Human/Drosophila) ============================================================== Part of Infogen database - Known genes of Human and Drosophila and Visualization of their functional signals is available at http://genomic.sanger.ac.uk/ These Infogene files and Java Viewer of Gene structures is design by Igor Seledtsov and Victor Solovyev for Infogen is designed as a resource of information about genes and their components Java Viewer will be used for a) Visually inspection of gene structure in Infogene entries of known or predicted genes b) In interactive Gene prediction in annotation genomic sequences from genome sequencing Projects HOW TO WORK WITH Genes_in_Pictures: see Help menu in Java Viewer: About Infogene format see Help menu in Java Viewer: Infogen Clicking by mouse you can see Infogen gene description (see Help: About) General Picture of GENBANK/INFOGENE content: HUMAN GENES IN GENBANK/INFOGENE: CDS total 34448 Partial CDS 20585 RNA CDS Total 24306 Partial RNA CDS 13329 DNA CDS Total 10142 Partial DNA CDS 7256 Exons Total 36674 Partial Exons 10985 Exons Total 36674 Genes Total 10142 Partial Genes 8226 Acceptor Site Total 26507 Acceptor Site standart 25902 ( 97.72%) Acceptor Site putative 3024 Acceptor Site putative standart 2949 ( 97.52%) Acceptor Site nonputative 23483 Acceptor Site nonputative standart 22953 ( 97.74%) Donor Site Total 22341 Donor Site standart 21916 ( 98.10%) Donor Site putative 2662 Donor Site putative standart 2596 ( 97.52%) Donor Site nonputative 19679 Donor Site nonputative standart 19320 ( 98.18%) Start codons 13854 Standart Start codons 13694 ( 98.85%) Stop codons 13810 Standart Stop codons 13810 (100.00%) CAAT-boxes /Total/Putative/Experimental 405 51 2 TATA-boxes /Total/Putative/Experimental 802 119 14 TSP (Cap sites) /Total/Putative/Experimental 2554 128 118 PolyA signals /Total/Putative/Experimental 3548 444 85 PolyA sites /Total/Putative/Experimental 2066 77 81 DROSOPHILA MELANOGASTER GENES IN GENBANK/INFOGENE: CDS total 3521 Partial CDS 1025 RNA CDS Total 1865 Partial RNA CDS 316 DNA CDS Total 1656 Partial DNA CDS 709 Exons Total 4648 Partial Exons 1840 Exons Total 4648 Genes Total 1656 Partial Genes 753 Acceptor Site Total 3043 Acceptor Site standart 2870 ( 94.31%) Acceptor Site putative 135 Acceptor Site putative standart 133 ( 98.52%) Acceptor Site nonputative 2908 Acceptor Site nonputative standart 2737 ( 94.12%) Donor Site Total 2014 Donor Site standart 1873 ( 93.00%) Donor Site putative 70 Donor Site putative standart 69 ( 98.57%) Donor Site nonputative 1944 Donor Site nonputative standart 1804 ( 92.80%) Start codons 2496 Standart Start codons 2475 ( 99.16%) Stop codons 2476 Standart Stop codons 2476 (100.00) CAAT-boxes /Total/Putative/Experimental 39 4 0 TATA-boxes /Total/Putative/Experimental 217 24 3 TSP (Cap sites) /Total/Putative/Experimental 539 10 35 PolyA signals /Total/Putative/Experimental 773 104 20 PolyA sites /Total/Putative/Experimental 420 7 19 -- Victor Solovyev The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK Email: solovyev@sanger.ac.uk http://genomic.sanger.ac.uk Phone: 44-1223-494799 FAX: 44-1223-494919 From owner-software@net.bio.net Thu Jul 08 15:46:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!dispose.news.demon.net!demon!colt.net!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.ox.ac.uk!not-for-mail From: James Cuff Newsgroups: bionet.software Subject: [ANNOUNCE] Secondary structure prediction mail list Date: Thu, 08 Jul 1999 17:40:15 +0100 Organization: European Bioinformatics Institute Message-ID: <3784D46F.167E@ebi.ac.uk> NNTP-Posting-Host: worf.molbiol.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.ox.ac.uk 931452016 2167 163.1.2.30 (8 Jul 1999 16:40:16 GMT) X-Complaints-To: newsmaster@ox.ac.uk NNTP-Posting-Date: 8 Jul 1999 16:40:16 GMT X-Mailer: Mozilla 3.0 (X11; I; OSF1 V4.0 alpha) Lines: 35 Dear colleagues, We are happy to announce a combined Jpred and secondary structure prediction discussion mailing list. It is planned that the list will act as forum for discussion of protein secondary structure prediction methods and sequence/structure analysis techniques. The mailing list will also be used to keep subscribers up to date with improvements to the Jpred secondary structure prediction WWW server. Announcements of new prediction methods and relevant papers on prediction are also very much welcomed. The jpredusers mailing list can be accessed by sending an e-mail to majordomo@ebi.ac.uk, with the body message containing the words: subscribe jpredusers More information can be found at: http://barton.ebi.ac.uk/ Best regards, James. p.s. Sorry if this message has popped out twice - we have been having problems with our newsfeed at the HGMP ----------------------------------------------------------------- James Cuff | European Bioinformatics Institute +44 (0) 1223 49 4607 | Wellcome Trust Genome Campus james@ebi.ac.uk | Hinxton, Cambridge. CB10 1SD, UK ----------------------------------------------------------------- From owner-software@net.bio.net Thu Jul 08 18:15:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!feeder.qis.net!nntp.abs.net!newsfeed.fast.net!uunet!ffx.uu.net!ffx4nh4!not-for-mail From: Jackie Spector Newsgroups: bionet.software Subject: Bio-Ontologies '99 Date: Thu, 08 Jul 1999 15:08:15 -0400 Organization: NetGenics Lines: 390 Message-ID: <3784F71F.19E40413@netgenics.com> NNTP-Posting-Host: relay.netgenics.com Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------749194EA5D56C4448950C21F" X-Trace: ffx2nh4.news.uu.net 931460776 465 63.69.121.194 (8 Jul 1999 19:06:16 GMT) X-Complaints-To: news@ffx2nh4.news.uu.net NNTP-Posting-Date: 8 Jul 1999 19:06:16 GMT X-Mailer: Mozilla 4.03 [en] (WinNT; I) This is a multi-part message in MIME format. --------------749194EA5D56C4448950C21F Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Bio-Ontologist: I would like to invite you to the Second Annual Bio-Ontologist Meeting (Bio-Ontologies 99), on August 5th in Heidelberg, Germany. This is immediately before ISMB-99 August 6-10 in Heidelberg. Last year's kick-off meeting was a great success, and was a clear indication of the general interest and support people had for Ontologies in the life sciences. The goal of this consortium is the identification and promotion of a practical set of technologies that will aid in the knowledge management and exchange of concepts and representations in the life sciences. This meeting will focus on current issues and activities that are described in more details below: --------------749194EA5D56C4448950C21F Content-Type: text/html; charset=us-ascii; name="bio_ontologies-99.html" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="bio_ontologies-99.html" Content-Base: "http://www-smi.stanford.edu/projects/b io-ontology/bio_ontologies-99.html" Bio Ontologies

Bio-Ontologies '99
Heidelberg, Germany
5 August 1999

WB00668_.gif (22594 bytes)

Announcing the Second Annual Bio-Ontologies Meeting
sponsor by NetGenics, Inc. and SmithKline Beechman

Fellow Bio-Ontologist:

I would like to invite you to the Second Annual Bio-Ontologist Meeting (Bio-Ontologies 99), on August 5th in Heidelberg, Germany. This is immediately before ISMB-99  August 6-10 in Heidelberg. Last year's kick-off meeting was a great success, and was a clear indication of the general interest and support people had for Ontologies in the life sciences. The goal of this consortium is the identification and promotion of a practical set of technologies that will aid in the knowledge management and exchange of concepts and representations in the life sciences. This meeting will focus on current issues and activities that are described in more details below:

Purpose and Scope

 

Many in the group have been active since our last meeting and an agenda is being planned that will include the work currently being done in the following areas:

  • Results from analyses and experiments on how to effectively exchange Ontologies, including a recommendation for a Common Ontologies Exchange Language
  • Presentation of ontologies produced by members from various genomics efforts (e.g. Flybase, Saccharomyces GD, Mouse GB, ACeDB, Arabidopsis DB
  • Specific uses of ontologies in research and drug discovery with special focus on Pre-Competitive Ontologies for the industry

We would like to invite others to present their work and views on both uses and  modeling of biological ontologies. Please submit abstracts for short talks or posters by July 1, 1999, to Eric Neumann, PhD. of NetGenics, Inc or Robin A. McEntire of SmithKline Beechman.

Some intended results of the meeting are:

  • Action items to focus on what ontological and knowledge-management tools are available
  • Work group addressing development of ontologies in particular areas of the Life Sciences, e.g. molecular biology, genetics, metabolic and signaling pathways, etc.
  • Further support from other bio-research groups, as well as backing from industry
  • Dissemination of information and results produced by this consortium

Facilities



The workshop will be held at the Marriott in Heidelberg which is one of the participating ISMB hotels and facilities. Attendees are expected to make their own arrangements for travel and accommodation (we assume most will simply extend their bookings for ISMB). For more info on hotels with special ISMB conference rates, see http://ismb99.gmd.de/hotel.html.

Registration & Fees



We have elected to charge a small fee to cover the incidental costs of organizing the workshop.  Registration fees will be $30 for students/postdocs, $45 for other academics and $60 for industry or commercial attendees. Registration includes coffee, tea, lunch and all workshop materials. Deadline for advanced registration is July 15.

  All fees should be made payable in US dollars to NetGenics Bio-Ontolgies '99 and mailed to:
NetGenics, Inc.
1717 East Ninth Street
Suite 1600
Cleveland, OH 44114
Attn: Bio-Ontologies '99

Important Dates to Remember
Registration begins:  May 1, 1999
Abstract submissions due: July 1, 1999
Bio-Ontologies final schedule: July 1, 1999
Registration and payment due: July 15, 1999
 

Go to Registration Form
Home

 

 

--------------749194EA5D56C4448950C21F-- From owner-software@net.bio.net Sat Jul 10 14:29:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!remarQ73!supernews.com!remarQ.com!news.usenetserver.com!uunet!ffx.uu.net!newsfeed.attap.net!infeed.jaring.my!not-for-mail From: "Khoo" Newsgroups: bionet.software Subject: Can anyone help me with this problem in Microsoft Access97 Date: Sat, 10 Jul 1999 23:28:37 +0800 Organization: Unconfigured Lines: 11 Message-ID: <7m7ohj$b11$1@news4.jaring.my> NNTP-Posting-Host: j37.sdk.jaring.my X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 I am Khoo from Malaysia. I am building a database for my school to record all the students names, address, and etc... Now I want to build a search engine for it to let user search for first names or the first alphabates of the name.... Please help me Sincerely Khoo From owner-software@net.bio.net Sun Jul 11 00:16:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!arclight.uoregon.edu!hammer.uoregon.edu!newsfeed.direct.ca!tank.news.pipex.net!pipex!uunet!ams.uu.net!ffx.uu.net!in5.uu.net!PM01NEWS!not-for-mail Message-ID: <3787EF0C.B985F1FE@mciworld.com> From: "Jeremy.Parsons" Reply-To: jparsons@hgmp.mrc.ac.uk X-Mailer: Mozilla 4.51 [en]C-CCK-MCD {MCIWORLDV2} (Win98; U) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software Subject: Re: Seeking: SCF-file (sequencing data) viewer for Mac! References: <3777B048.A2EA0A67@uni-tuebingen.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 19 Date: Sun, 11 Jul 1999 01:09:15 GMT NNTP-Posting-Host: 208.252.164.133 X-Trace: PM01NEWS 931655355 208.252.164.133 (Sun, 11 Jul 1999 01:09:15 GMT) NNTP-Posting-Date: Sun, 11 Jul 1999 01:09:15 GMT You might want to try a Java trace viewer: have a look around http://www.ebi.ac.uk/~jparsons jeremy Eric Beitz wrote: > Hi all, > > is there a freeware viewing software for so-called SCF-files for the > Macintosh? These files are produced by our LiCor sequencer (OS2) and contain > the graphical display of the sequencing raw data. I want to analyse the data > on my PowerBook which is much more convenient for me. > > Any sugestions welcome! > > Thanks, > Eric From owner-software@net.bio.net Sun Jul 11 00:22:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!yellow.newsread.com!netaxs.com!newsread.com!newspeer1.nac.net!news.new-york.net!uunet!ffx.uu.net!in5.uu.net!PM01NEWS!not-for-mail Message-ID: <3787F071.9C67FA87@mciworld.com> From: "Jeremy.Parsons" Reply-To: jparsons@hgmp.mrc.ac.uk X-Mailer: Mozilla 4.51 [en]C-CCK-MCD {MCIWORLDV2} (Win98; U) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software Subject: Re: ABI electrophoretograms on PC=>what about assembly programs? References: <3771B469.2B3A1680@flinders.edu.au> <3778b1c8.18163102@news.iastate.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 33 Date: Sun, 11 Jul 1999 01:15:11 GMT NNTP-Posting-Host: 208.252.164.133 X-Trace: PM01NEWS 931655711 208.252.164.133 (Sun, 11 Jul 1999 01:15:11 GMT) NNTP-Posting-Date: Sun, 11 Jul 1999 01:15:11 GMT You can view using a Java trace viewer: http://www.ebi.ac.uk/~jparsons but if you just use files on a PC. and want editing, you would be better off with the Staden group's Trev http://www.mrc-lmb.cam.ac.uk/pubseq/index.html If you want an assembler, you could try Staden's Gap4, phrap/consed, Cap3 etc Jeremy Chris Kafer wrote: > What we really need is an assembly program for PCs, like > Autoassembler, that will take the electropherogram files. Anyone know > of freeware/shareware or websites that will do this? I've found one > that will take fasta formats but what a pain to have to take 40 or > more text sequences and reformat them. > > On 23 Jun 1999 21:35:28 -0700, Lee.Smith@FLINDERS.EDU.AU (Lee Smith) > wrote: > > >Hi > >This may well be covered in a FAQ, but then I can't find that either! > >Does anyone have any suggestions for software to allow editing/viewing > >of > >the electrophoretograms produced by an ABI sequencer on a PC? > >Obviously shareware/freeware prefered! > > > >Lee Smith > >Flinders University > >SA 5042 > >Australia > > > >Lee.Smith@flinders.edu.au > > From owner-software@net.bio.net Mon Jul 12 13:07:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!infeed.is.co.za!feeder.is.co.za!hermes.is.co.za!not-for-mail From: "winhide" Newsgroups: bionet.software Subject: SANBI executables Date: Mon, 12 Jul 1999 15:56:15 +0200 Organization: An Internet Solution Customer Lines: 78 Message-ID: <7mcs82$qn3$1@hermes.is.co.za> References: <37830D77.323B1FD@gerga.sun.ac.za> NNTP-Posting-Host: yebo.sanbi.ac.za Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0088_01BECC7F.126B7E20" X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_0088_01BECC7F.126B7E20 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable SA Specific: We are supporting Linux executables, the first, are those that are = already supported at Pasteur Institute. Please feel free to subscribe to = the SA bioinformatics news group at: fourie@sanbi.ac.za )if you are in = SA) Win Gian van der Spuy wrote in message = <37830D77.323B1FD@gerga.sun.ac.za>... Based on advice from this group I have downloaded and compiled = namot. I have also installed the xview libraries and binaries. I am = quite new to Linux so pardon me if this is a silly question, but how do = I now run xview and get namot running in it.=20 --=20 Gian van der Spuy=20 Molecular and Cellular Biology=20 University of Stellenbosch=20 South Africa=20 =20 ------=_NextPart_000_0088_01BECC7F.126B7E20 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
SA = Specific:
 
We are supporting Linux executables, = the first, are=20 those that are already supported at Pasteur Institute. Please feel free = to=20 subscribe to the SA bioinformatics news group at: fourie@sanbi.ac.za )if you are in = SA)
 
Win
Gian van der Spuy wrote in message <37830D77.323B1FD@gerga.s= un.ac.za>...
Based=20 on advice from this group I have downloaded and compiled namot. I = have also=20 installed the xview libraries and binaries. I am quite new to Linux = so=20 pardon me if this is a silly question, but how do I now run xview = and get=20 namot running in it.=20

--
Gian van der Spuy
Molecular and Cellular Biology=20
University of Stellenbosch
South Africa
 =20

------=_NextPart_000_0088_01BECC7F.126B7E20-- From owner-software@net.bio.net Mon Jul 12 14:39:00 1999 Path: biosci!sanger.ac.uk!solovyev From: solovyev@sanger.ac.uk ("Victor Solovyev") Newsgroups: bionet.software Subject: Plant and Nematode HMM GeneFinders (FGENESH) Date: 12 Jul 1999 08:39:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 59 Sender: daemon@net.bio.net Distribution: world Message-ID: <9907121633.ZM5617@octane> NNTP-Posting-Host: net.bio.net We installed New PLANT AND NEMATODE specific gene-finding for HMM based program FGENESH for multiple gene prediction in genomic DNA (in addition to HUMAN AND DROSOPHILA gene predictors) It is available at http://genomic.sanger.ac.uk/ of our Computational Genomic Group WEB server (http://genomic.sanger.ac.uk/gf/gf.html) Accuracy of the program is about 90% at the nucleotide level to predict coding exons (AC = 0.5 (Sn + Sp)). TO USE specific version click Plant or Nematode button + fgenesh button Past your sequence to the window or load your file with sequence in FASTA fromat Example of output of the program: fgenesh Mon Jul 12 16:28:07 BST 1999 FGENESH 1.0 Prediction of potential genes in Plant(Dct) genomic DNA Time: Mon Jul 12 16:28:07 1999 Seq name: CGG WEB SERVER PAST Sequence Length of sequence: 4253 GC content: 37 Zone: 1 Number of predicted genes 1 in +chain 1 in -chain 0 Number of predicted exons 3 in +chain 3 in -chain 0 Positions of predicted genes and exons: G Str Feature Start End Score ORF Len 1 + TSS 15 -3.75 1 + 1 CDSf 1681 - 1984 42.43 1681 - 1983 303 1 + 2 CDSi 2162 - 2634 63.01 2164 - 2634 471 1 + 3 CDSl 2733 - 3584 99.84 2733 - 3584 852 1 + PolA 4001 -0.45 Predicted protein(s): >FGENESH 1 3 exon (s) 1681 - 3584 542 aa, chain + MAKKGKEVLNALDAAKTQMYHFTAIVIAGMGFFTDAYDLFSISLVTKLLGRIYYHVDSSK KPGTLPPNVAAAVNGVAFCGTLAGQLFFGWLGDKLGRKKVYGITLMLMVLCSLGSGLSFG HSANGVMATLCFFRFWLGFGIGGDYPLSATIMSEYANKKTRGAFIAAVFAMQGFGILAGG IVSLIVSSTFDHAFKAPTYEVDPVGSTVPQADYVWRIVLMFGAIPALLTYYWRMKMPETA RYTALVARNTKQAASDMSKVLQVDLIAEEEAQSNSNSSNPNFTFGLFTREFARRHGLHLL GTTTTWFLLDIAYYSSNLFQKDIYTAIGWIPAAETMNAIHEVFTVSKAQTLIALCGTVPG YWFTVAFIDILGRFFIQLMGFIFMTIFMFALAIPYDHWRHRENRIGFLIMYSLTMFFANF GPNATTFVVPAEIFPARLRSTCHGISAASGKAGAIVGAFGFLYAAQSSDSEKTDAGYPPG IGVRNSLLMLACVNFLGIVFTLLVPESKGKSLEEISREDEEQSGGDTVVEMTVANSGRKV PV -- Victor Solovyev The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK Email: solovyev@sanger.ac.uk http://genomic.sanger.ac.uk Phone: 44-1223-494799 FAX: 44-1223-494919 From owner-software@net.bio.net Tue Jul 13 14:53:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newshub.sdsu.edu!not-for-mail From: Neill White Newsgroups: bionet.software Subject: Biomer : MM/MD on the web Date: Tue, 13 Jul 1999 15:56:13 +0000 Organization: The Scripps Research Institute Lines: 25 Message-ID: <378B619D.8449288@scripps.edu> NNTP-Posting-Host: harpo-p31.sdsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Server-Date: 13 Jul 1999 15:47:44 GMT X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.36 i586) X-Accept-Language: en Dear Colleagues, This is an announcement of the availability of a new molecular modeling program - Biomer - that is accessible over the web. It should be useful as an educational tool as well as a means to generate structures quickly and easily. It is written in Java, and version 1.0a has the following features: Model Builders for: nucleic acids (DNA/RNA) polypeptides polysaccharides Interactive molecule editor with fragment libraries Implementation of the AMBER force field Geometry Optimization with steepest descent / conjugate gradient Simulated Annealing with molecular dynamics Reads / Writes PDB files Exports jpeg, gif, and ppm images It is located at http://www.scripps.edu/~nwhite/Biomer/index.html Regards, Neill White From owner-software@net.bio.net Wed Jul 14 16:29:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!cs.utexas.edu!news.uh.edu!news.uth.tmc.edu!not-for-mail From: Markus Hoenicka Newsgroups: bionet.software Subject: Q: free restriction analysis software Date: 14 Jul 1999 12:10:02 +0000 Organization: University of Texas Health Science Center Lines: 21 Sender: mhoen@GIRCH19 Message-ID: NNTP-Posting-Host: girch72.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: Gnus v5.5/Emacs 20.3 I'd like to have a simple tool for restriction analysis, i.e I feed a sequence file to it and a list of restriction enzymes, and the tool tells me the number and location of the restriction sites, the length of the released fragments etc. It should run on Windows NT, but console applications, incl ANSI C Unix source code, and perl scripts are actually preferred. Is anyone aware of such a thing? TIA Markus -- Markus Hoenicka UT Houston Medical School Dept. of Integrative Biology and Pharmacology 6431 Fannin MSB4.114 Houston, TX 77030 (713) 500-6313, -7476, -7477 (713) 500-7444 (fax) mhoen@farmr1.med.uth.tmc.edu http://ourworld.compuserve.com/homepages/hoenicka_markus From owner-software@net.bio.net Wed Jul 14 16:54:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Q: free restriction analysis software Date: 14 Jul 1999 17:48:34 GMT Organization: Biology, Indiana University - Bloomington Lines: 29 Message-ID: <7miihi$psj$1@jetsam.uits.indiana.edu> References: NNTP-Posting-Host: chipmunk.bio.indiana.edu Sounds like you want Harry Mangalam's nice 'tacg' program. The below readme may be a bit old, but should get you going. -- Don tacg: a program for the restriction enzyme analysis of DNA, V 1.7 by Harry Mangalam, UC Irvine (mangalam@uci.edu, 714 824 4824) This file announces the availability and describes the basic functionality of 'tacg', a command line tool for the restriction enzyme analysis of DNA for unix-like operating systems. There is a Web page describing it more fully at: http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg.main.html There is also a WWW interface to it so that you can try it out and see if it's worth downloading: http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg.form.html The complete code to implement the Web interface is also available (tho not as well debugged as the program itself) at: http://hornet.bio.uci.edu/~hjm/projects/tacg/tacgi You can always get the latest version in ANSI C source code and several pre-compiled binaries (unless I move) at: ftp://mamba.bio.uci.edu/pub/tacg/ -- -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Jul 14 18:05:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!newsfeed.slurp.net!not-for-mail Message-ID: <378CDF0F.39FE6189@qualityiskey.com> From: support@qualityiskey.com Reply-To: support@qualityiskey.com Organization: Quality Is Key Ltd. X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: sci.med.laboratory,sci.med.pathology,sci.bio.technology,bionet.software Subject: CostCrusher LabAudit- Get your costs right to get your decisions right. Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Lines: 119 Date: Wed, 14 Jul 1999 15:03:43 -0400 NNTP-Posting-Host: 209.91.129.74 X-Trace: newsfeed.slurp.net 931978671 209.91.129.74 (Wed, 14 Jul 1999 13:57:51 CDT) NNTP-Posting-Date: Wed, 14 Jul 1999 13:57:51 CDT CostCrusher LabAudit Get your costs right to get your decisions right. What is it? --------------- CostCrusher LabAudit is a tool to help you and your staff to make better decisions. The system models any lab environment so is ideal for auditing and comparing costs generated by suppliers, customers, tests and samples performed across workstations or disciplines. With CostCrusher you can focus and answer key cost and performance questions within the lab’s operations and customer services. CostCrusher uses the latest Activity Based Costing techniques to avoid the cost distortion problems inherent in traditional cost systems (Excel like spreadsheets) that lead to misguided decisions. Why CostCrusher? -------------------------- A modern costing system should: 1) Uncover & prioritize problems to tackle and solve. 2) Identify opportunities to exploit. 3) Influence the behaviour of people. 4) Stimulate staff to achieve better results - evaluate their own performance. CostCrusher LabAudit introduces a more modern, more relevant management approach to costs & productivity. How does it work? ------------------------- Most cost systems tell one person what was spent from the budget. CostCrusher shows each user (in real time): ==> Where, why and how the budget is being spent in their area of responsibility. ==> Their personal impact on the lab’s cost & productivity. This helps to make costs transparent and each individual to make better decisions in managing their own area. It encourages a change in behaviour and raises each person’s productivity leading to (a) an overall lowering of costs and (b) a feeling of greater responsibility & motivation. Profit & Loss - A More Transparent View -------------------------------------------------------- CostCrusher LabAudit demonstrates a true profit of $ 4.80 where a profit of $ 11.76 was falsely perceived ! Traditional Costing | CostCrusher LabAudit | Price or Budget for Sample 35.20 | Price or Budget for Sample 35.20 Direct Material Costs 7.25 | Direct Material Costs 8.50 | | Gross Profit 27.95 | Gross Profit 26.70 | | Less | Less ------------------------ | -------------------------- Indirect Material 1.57 | Sample Reception & Handling 2.70 Personnel 6.06 | Consumables Preparation 1.30 Overheads 8.56 | Production 3.20 | Maintenance & Waste Handling 2.40 | Supplies Management 4.10 | Marketing & Services 2.80 | Customer Administration 5.40 | 16.19 | 21.90 | Profit (coverage) 11.76 | Profit (coverage) 4.80 ===== | ===== | Less Business Sustaining 2.90 | Costs | 1.90 | ===== For more information contact: Michael Piccirillo TISMO General Wille-Strasse Postfach 180 CH-8706 Feldmeilen Phone: 41-01-923 82 44 Fax: 41-01-923 77 43 Email: saveit@tismo.com Website: http://www.costcrusher.com _______________________________________ Zoe Brooks QIK Quality Is Key Ltd. Phone: (705)866-2074 Toll free Canada & USA: 1-888-222-6252 Fax: (705)866-2287 Email: qikinfo@qualityiskey.com Website: http://www.qualityiskey.com From owner-software@net.bio.net Wed Jul 14 18:09:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!cs.utexas.edu!news.uh.edu!news.uth.tmc.edu!not-for-mail From: Markus Hoenicka Newsgroups: bionet.software Subject: Re: Q: free restriction analysis software Date: 14 Jul 1999 14:04:34 +0000 Organization: University of Texas Health Science Center Lines: 13 Sender: mhoen@GIRCH19 Message-ID: References: <7miihi$psj$1@jetsam.uits.indiana.edu> NNTP-Posting-Host: girch72.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: Gnus v5.5/Emacs 20.3 I guess that's what I'm looking for! Thanks Markus -- Markus Hoenicka UT Houston Medical School Dept. of Integrative Biology and Pharmacology 6431 Fannin MSB4.114 Houston, TX 77030 (713) 500-6313, -7476, -7477 (713) 500-7444 (fax) mhoen@farmr1.med.uth.tmc.edu http://ourworld.compuserve.com/homepages/hoenicka_markus From owner-software@net.bio.net Wed Jul 14 19:48:00 1999 Path: biosci!olivet.edu!C-Stanley From: C-Stanley@olivet.edu (Conrad Stanley) Newsgroups: bionet.software Subject: (no subject) Date: 14 Jul 1999 13:48:49 -0700 Organization: Governors State University Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <378CADEB.568A0EFE@olivet.edu> Reply-To: C-Stanley@uxa.ecn.bgu.edu NNTP-Posting-Host: net.bio.net I am researching prairie pollinators and am in desperate need of a key!!!!!! Could you assist me???? Conrad Stanley constanley@juno.com From owner-software@net.bio.net Wed Jul 14 21:04:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!cyclone.mbnet.mb.ca!canopus.cc.umanitoba.ca!not-for-mail From: Brian Fristensky Newsgroups: bionet.software Subject: Re: Q: free restriction analysis software Date: Wed, 14 Jul 1999 16:58:12 -0500 Organization: University of Manitoba Lines: 72 Message-ID: <378D07F4.A2540AF6@cc.umanitoba.ca> References: NNTP-Posting-Host: brassica.cc.umanitoba.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: canopus.cc.umanitoba.ca 931989493 4981 130.179.16.121 (14 Jul 1999 21:58:13 GMT) X-Complaints-To: Postmaster@cc.umanitoba.ca NNTP-Posting-Date: 14 Jul 1999 21:58:13 GMT X-Mailer: Mozilla 4.6 [en] (X11; U; SunOS 5.5.1 sun4u) X-Accept-Language: en Markus Hoenicka wrote: > > I'd like to have a simple tool for restriction analysis, i.e I feed > a sequence file to it and a list of restriction enzymes, and the tool > tells me the number and location of the restriction sites, the length > of the released fragments etc. > > It should run on Windows NT, but console applications, incl ANSI C Unix > source code, and perl scripts are actually preferred. > > Is anyone aware of such a thing? > TIA > Markus > -- The FSAP package includes text-based interactive programs for restriction site searches which either let you type in the name and sequence for one restriction enzyme at a time (INTREST) or read in a restriction recognition sequence file (eg. REBASE) for a batch search (BACHREST): http://www.umanitoba.ca/afs/plant_science/UNIX/doc/fsap/rest.asc INTREST and BACHREST correctly handle circular sequences, and tell you the termini, based on known cutting sequences. BACHREST can also be run from Steven Smith's GDE interface. One of the nice features of INTREST and BACHREST is that IUPAC-IUB ambiguity codes can even appear in the target sequence. In addition to letting you to search for cutting sites in things like consensus sequences or sequences with ambiguities, you can build model sequences that are composites of known sequence, N's, and known restriction sites. For example, GGATCCCTGGATAGGAATCNNNNNNNNNNNNNNNNNNGANTCNNNNNNNNNNNNNNNGATTCCTAG would give you an output correctly showing the Hinf1 (GANTC) fragments. This approach is often useful if you have a construct for which the vector sequence is known, but some or all of the insert sequence is unknown. The insert can be simulated by a combination of N's and restriction sites, which lets you predict the fragments you should see on a gel. DIGEST reads in output files produced by BACHREST, and lets you perform multiple enzyme digests, either partial or complete. Again, BACHREST gives you a table listing fragment sizes, and cutting enzymes and positions of cuts for termini. http://www.umanitoba.ca/afs/plant_science/UNIX/doc/fsap/digest.asc C-source code or Sun/Solaris binaries for the FSAP package are available at: http://home.cc.umanitoba.ca/~psgendb/FSAP.html An old MS-DOS version is also available. -- =========================================================================== Brian Fristensky | ... because computer vendors look at Department of Plant Science | higher education as a potentially University of Manitoba | huge revenue source ... there would Winnipeg, MB R3T 2N2 CANADA | ultimately be only five universities frist@cc.umanitoba.ca | worldwide - and they would be Office phone: 204-474-6085 | Microsoft, Disney... you get the FAX: 204-261-5732 | picture. http://home.cc.umanitoba.ca/~frist/ Wendy Grossman, Sci. Am. July 1999 =========================================================================== From owner-software@net.bio.net Wed Jul 14 22:16:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.tli.de!blackbush.xlink.net!news-kar1.dfn.de!news-han1.dfn.de!news-ham1.dfn.de!news.rz.uni-kiel.de!not-for-mail From: Klaus Schnack Newsgroups: bionet.software Subject: Prog. for shade matrix from species-station table Date: Tue, 13 Jul 1999 00:28:46 +0200 Organization: Rechenzentrum der Universitaet Kiel, Germany Lines: 26 Message-ID: <378A6C1E.167E@sfb313.uni-kiel.de> NNTP-Posting-Host: piggy.sfb313.uni-kiel.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (X11; I; AIX 2) Hi, to examine species distributions I'm looking for a program to create a shade-matrix from a species-station table, i.e. to replace each count in the table with a symbol whichs size (or shade) is proportional to the value. It's a common procedure to compare species distribution between different sites, but until now I didn't find a handy tool for this task. Any suggestion where to find such a tool would be appreciated very much. Thanks Klaaus ''' (0 0) ---------------------------oOO----(_)----OOo---------------------------- Klaus Schnack ks@sfb313.uni-kiel.de Institut fuer Polaroekologie Wischhofstr. 3, Geb. 12 24148 Kiel, Germany ------------------------------------------------------------------------ From owner-software@net.bio.net Wed Jul 14 22:19:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!remarQ73!supernews.com!remarQ.com!remarQ69!WReNclone!WReNphoon3.POSTED!WReN!not-for-mail From: Klaus Schnack Newsgroups: bionet.software Subject: Req: Prg. for shade matrix Organization: http://www.remarq.com: The World's Usenet/Discussions Start Here X-Originating-Host: 134.245.39.102 X-Wren-Trace: cDcQMCU3awkhc2MVJ3t2b3FkdmdoZiJ7YG54ZWd6dzdpYiN4ayN3d2hvfWNpJWQ3JDQ5PSxhIDc5N3o/LXttPD16 Message-ID: <931992925.19249@www.remarq.com> Lines: 24 Date: Wed, 14 Jul 1999 14:55:22 -0800 NNTP-Posting-Host: 10.0.3.195 X-Complaints-To: wrenabuse@remarq.com X-Trace: WReNphoon3 931993726 10.0.3.195 (Wed, 14 Jul 1999 16:08:46 PDT) NNTP-Posting-Date: Wed, 14 Jul 1999 16:08:46 PDT Hi, to examine species distributions I'm looking for a program to create a shade-matrix from a species-station table, I.e. to replace each count in the table with a symbol whichs size (or shade) is proportional to the value. It's a common procedure to compare species distribution between different sites, but until now I didn't find a handy tool for it. Any suggestion where to find such a tool would be appreciated Thanks Klaus Schnack wrobeli(no spam)hotmail.com **** Posted from RemarQ - http://www.remarq.com - Discussions Start Here (tm) **** From owner-software@net.bio.net Thu Jul 15 07:11:00 1999 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.32.206.55!newsfeed.berkeley.edu!oleane!jussieu.fr!saphir.jouy.inra.fr!lindenb From: lindenb@jouy.inra.fr (Pierre Lindenbaum) Newsgroups: bionet.software Subject: Re: Q: free restriction analysis software Date: 15 Jul 1999 07:44:48 GMT Organization: INRA Lines: 253 Message-ID: <7mk3hg$9n5$1@saphir.jouy.inra.fr> References: <378D07F4.A2540AF6@cc.umanitoba.ca> NNTP-Posting-Host: biotec.jouy.inra.fr X-Newsreader: TIN [version 1.2 PL2] : Markus Hoenicka wrote: : > : > I'd like to have a simple tool for restriction analysis, i.e I feed : > a sequence file to it and a list of restriction enzymes, and the tool : > tells me the number and location of the restriction sites, the length : > of the released fragments etc. : > Here is a description of my online program called 'CloneIt'. I hope it will help you... Pierre LINDENBAUM ------------------------------------------------------------------------------ _________________________________________________________________ CLONEIT(tm) ONLINE VERSION A WEB BASED INTERFACE FINDING SUB-CLONING STRATEGIES, IN-FRAME DELETIONS AND FRAMESHIFTS USING RESTRICTION ENZYMES AND DNA POLYMERASES. http://topaze.jouy.inra.fr/cgi-bin/CloneIt/CloneIt _________________________________________________________________ What is CloneIt ? The use of plasmid vectors in cloning strategies is the basis of any molecular biologist repertoire. Efficiency is essential and requires the use of the most appropriate restriction enzymes choices for the desired application. Selection of those enzymes remains a skill. Several points that merit consideration include (1) the enzymes characteristics, (2) location of the restriction sites within the sequence, (3) complementarity of protuding ends, (4) possible self ligation, (5) use of modifying DNA polymerase generating blunt ends, (6) in frame cloning constraints,(7) use of partial digestions and (8) the creation of a stop codon at the ligation site. This exercise is labor intensive, even with the help of the classical DNA analysis softwares. These programs typically facilitate localizing restriction sites in a plasmid sequence; however it is impossible to examine all restriction sites and /or combinations then, a simple cloning strategy may be over-looked as a result of incomplete or inadequate searching. CloneIt Online was created in order to quickly find cloning strategies (including sub-cloning, in-frame deletions and frameshifts) while controlling the problems described above. CloneIt Online is available at the following URL: http://topaze.jouy.inra.fr/cgi-bin/CloneIt/CloneIt ---------------------------------------------------------------------------- Samples ---------------------------------------------------------------------------- SubCloning ............................................................................ CloneIt V1.0 has found a solution: Digest VECTOR with EcoRI [G^AATTC] (878) and Sal I [g^tcgac] (894). 5' --G.CCG.G/AA.TT C.CCG.GGG.ATC.CG/T.CGA. CCT.GCA.GCC.AAG-- 3' 3' --C.GGC.C TT.AA/G.GGC.CCC.TAG.GC A.GCT./GGA.CGT.CGG.TTC-- 5' NH2 P E F P G I R R P A A K .COOH Digest first with EcoRI .Then treat with Klenow DNA polymerase. Finally digest with Sal I . Digest INSERT with Sca I [AGT^ACT] (1034) and Sal I [g^tcgac] (3605). 5' --AT.AAA.GT/ A.CTT.TCA.AAG.AAA.G-- --TA.GAG./TCG.A CC.TGC.AGG.CAT.G-- 3' 3' --TA.TTT.CA/ T.GAA.AGT.TTC.TTT.C-- --AT.CTC. AGC.T/GG.ACG.TCC.GTA.C-- 3' NH2 K V L S K K E - -- E S T C R H A .COOH Treat with T4 DNA polymerase. Sites wil be in frame ligated in 5'. The first stop codon detected BEFORE the EcoRI site (878) is localized at position 428 on vector. The first stop codon detected AFTER the Sca I site (1034) is localized at position 3558 on insert. Digestion post-ligation: no enzyme was found. ....................................................................... Finding in-frame deletions ....................................................................... CloneIt has found an in-frame deletion: Digest INSERT with Bcl I [t^gatca] (1427) and PstI [CTGCA^G] (3611). 5' --TG.TAT./GAT.C AG.GTT.CTT.ACT.G-- --CG.ACC. TGC.A/GG.CAT.GCA.AGC.T-- 3' 3' --AC.ATA. CTA.G/TC.CAA.GAA.TGA.C-- --GC.TGG./ACG.T CC.GTA.CGT.TCG.A-- 5' NH2 Y D Q V L T E -- -- T C R H A S F .COOH Treat with T4 DNA polymerase. Cloning boxes boundaries :[880-1155] [3359-3634]. Original: 5' ================================================ 3' Deletion: 5' =========......................................= 3' Equivalent to a deletion of 728 amino acids [79 %] Digestion post-ligation: BamHI Sal I Acc I Nsi I . The first stop codon detected AFTER the PstI site (3611) is localized at position 3639 on insert. Translated truncated sequence:... NSSSVPGAIKGSMAYRKRGARREANINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVV TDSQEEIKIADEVKKSTKEESKQLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLE DIKPEQAKKQTKLFRIFEPRQLPIYRANGEKELRNRTYTKLKKDTLPGDYDVREYFLNLY DR---------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --HASFCS... ......................................................................... Finding frameshifts in INSERT. ......................................................................... CloneIt has found an Enzyme that could induce frameshift. Digest INSERT with AccI [gt^mkac] (1659). 5' --.ATC.AGT.//AT A.CAC.ATA.AAT.GAT-- 3' 3' --.TAG.TCA. TA//T.GTG.TAT.TTA.CTA-- 5' NH2 I S I H I N D .COOH Treat with Klenow DNA polymerase. Beware : AccI [1 partial site] . After digestion, fill-in and ligation: 5' .ATC.AGT.ATA.TAC.ACA.TAA.ATG 3' 3' .TAG.TCA.TAT.ATG.TGT.ATT.TAC 5' NH2 I S I Y T * M COOH ¥ FrameShift (+ 2) ¥ 2 bases Added. ¥ Site is NOT reconstitued after ligation. ¥ [51 %] percentage of Insert. FIGURE: ========================= | (+2) =========================== Translated sequence:...EFELGTRGSMATFKDACYHYKRLNKLNSLVLKLGANDETRPAPMTKYKGTCL YTNLTYCRGCALYHVCQTCSQYNRCFLDEEPHLLRMRTFKDVVTKEDIEGLLTMYETLFPINEKLVNKFINSVKQ EYLLETYNHLLMPITLQALTINLEDNVYYIFGYYDCMEHENQTPFQFINLLEKYDKLLLDDRNFHRMSHLPVILQ RYFSKSRFLSKGKKRLSRSDFSDNLMEDRHSPTSLMQVVRNCISiyT*... ............................................................................ Informations ............................................................................ Get information about Bst1107 I INSERT Pattern -------------- Bst1107I [GTA^TAC] (1659) p5_1 digestion. 1 4652 pb Bst1107I 1744 - Bst1107I 1659 2 85 pb Bst1107I 1659 - Bst1107I 1744 ........................................................................... . Prototype :SnaI Microorganism :Bacillus stearothermophilus RFL1107 Source :A.A. Janulaitis Methylation site : Commercial availability : Angewandte Gentechnologie Systeme Fermentas AB Takara Shuzo Co. Ltd. Boehringer-Mannheim New England Biolabs Refs :457 ......................................................................... Looking for Isoschizomers. (*):Commercialy available) ( ) BspM90I GTA^TAC. (*) BssNAI GTA^TAC. also available at: SibEnzyme Ltd. ( ) BstBSI GTA^TAC. (*) BstZ17I GTA^TAC. also available at: New England BioLabs ( ) XcaI GTA^TAC. ........................................................................... Restriction Map ........................................................................... SACI SALI ECORI : hincii styi acsi : acci ECO52I NCOI alwi : ECL136II eaei bstdsi xhoii : bsp1286i bsh1285i MSCI xmni BAMHI : banii : NOTI eaei ecorv : vspi alwi : alw21i : HINDIII: : : : : : :: : : : : :: TGGCCATGGATATCGGAATTAATTCGGATCCGAATTCGAGCTCCGTCGACAAGCTTGCGGCCGCA \ 5266 ¥ ¥ ¥ ¥ ¥ ¥ ¥ \ ACCGGTACCTATAGCCTTAATTAAGCCTAGGCTTAAGCTCGAGGCAGCTGTTCGAACGCCGGCGT \ 5330 T P T :I S E :L I R::I R: I R: A P :S T :S L :R P H -> :A :M D: I G :I: N S D: P N S S S V: D K: L A::A A L -> : H: G Y R N: * F G :S E :F E :L R R Q A C G: R T -> : P: V $ L R: L * A :$ A :* A :R P L Q E F A: P T ........................................................................... Intersections ........................................................................... _______________________________ | VECTOR | INSERT | _______________________________ | IN | OUT | IN | OUT | ___________________________________________________________ AatII [GACGT^C ] | 0 | 1 | 0 | 1 | AccI [GT^MKAC ] | 1 | 3 | 1 | 3 | AccIII [T^CCGGA ] | 0 | 0 | 0 | 0 | Acc65I [G^GTACC ] | 0 | 1 | 2 | 0 | AccBSI [CCGCTC(-3/-3) ] | 0 | 3 | 0 | 3 | (...) VspI [AT^TAAT ] | 0 | 6 | 3 | 6 | XbaI [T^CTAGA ] | 0 | 0 | 2 | 1 | XcmI [CCANNNNN^NNNNT] | 0 | 2 | 0 | 0 | XhoI [C^TCGAG ] | 0 | 0 | 0 | 1 | XhoII [R^GATCY ] | 2 | 7 | 2 | 6 | XmaI [C^CCGGG ] | 1 | 0 | 1 | 0 | XmnI [GAANN^NNTTC ] | 0 | 4 | 0 | 3 | ___________________________________________________________ | IN | OUT | IN | OUT | _______________________________ | VECTOR | INSERT | _______________________________ From owner-software@net.bio.net Sat Jul 17 05:01:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!news1.best.com!news3.best.com!nntp1.ba.best.com!not-for-mail Reply-To: "www.genomejobs.com" From: "www.genomejobs.com" Newsgroups: bionet.software Subject: List of Bioinformatics jobs available listed at www.genomejobs.com 7/16/99 Date: Fri, 16 Jul 1999 22:39:25 -0700 X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Lines: 187 Message-ID: <379018cb$0$213@nntp1.ba.best.com> NNTP-Posting-Host: dynamic38.pm07.sf3d.best.com X-Trace: nntp1.ba.best.com 932190411 213 209.24.235.166 List of Bioinformatics jobs available listed at www.genomejobs.com 7/16/99 We advertise jobs in Genomics, Bioinformatics, Biotech, and other cutting edge life science areas where biology meets computers and micro-robotics. If this page does not load, just go to www.genomejobs.com/jobs.htm These are GREAT OPPORTUNITIES with GREAT COMPANIES!!!!!! _________________________________________________ 3rd Millennium Cambridge, MA http://www.genomejobs.com/jobs/3rd.htm Database Project Manager Web Applications Developer Bioinformatics Manager Affymetrix Santa Clara, CA http://www.genomejobs.com/jobs/affymetrix.htm Senior Scientist/Manager Staff Scientist Albert Einstein College of Medicine Bronx, NY http://www.genomejobs.com/jobs/einstein.htm Bioinformatics Associate American Cyanamid Princeton, NJ http://www.genomejobs.com/jobs/ac.htm Biologist - Biotechnology Ariad Pharmaceuticals, Cambridge MA http://www.genomejobs.com/jobs/ariad.htm Senior Scientist - Gene Expression Informatics Bioinformatics Scientist Senior Bioinformatics Scientist/Group Leader Axys Pharmaceuticals S. San Francisco, CA http://www.genomejobs.com/jobs/axys.htm Analytical Chemistry: Research Associate Chemistry: Sr. Research Associate Research Associate. Combinatorial Chemistry: Computational Chemist Synthetic/Organic Chemists-Ph.D & BS/MS Caliper Technology, Mountain View, CA http://www.genomejobs.com/jobs/caliper.htm Chemistry: Manager, Applications & Customer Support Chemistry: Production Development Chemist Chemistry: Senior Scientist - Cell Biology Chemistry: Senior Scientist - Enzymology Engineer: EE/Firmware Engineer Engineering: Electronic Engineering Technician Engineering: Software Engineer Engineering: Software Engineer - Data Analyst General Admin: Dir. of Human Resources Marketing: Vice President, S