Boxit-Database for Molecular Biology Laboratories

From owner-bio-software@hgmp.mrc.ac.uk Thu Jun 1 05:53:09 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 09B1917ABA; Thu, 1 Jun 2000 05:53:08 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 9725E17A56; Thu, 1 Jun 2000 05:53:07 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1AC2C415D5 for ; Thu, 1 Jun 2000 05:53:07 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id FAA09858 for bio-software-list@hgmp.mrc.ac.uk; Thu, 1 Jun 2000 05:53:06 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: sspen@newmail.net ("Rob Saky") X-Newsgroups: bionet.software Subject: FREE INFORMATION #150F Date: 1 Jun 2000 05:53:05 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 52 Message-ID: <20000601045300.F08A1415D5@mercury.hgmp.mrc.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable X-Trace: niobium.hgmp.mrc.ac.uk 959835185 9856 193.62.192.80 (1 Jun 2000 04:53:05 GMT) X-Complaints-To: news@net.bio.net X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A8DA517A56; Thu, 1 Jun 2000 05:53:02 +0100 (BST) X-Received: from pop.metalink.com.br (unknown [200.251.246.81]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id F08A1415D5 for ; Thu, 1 Jun 2000 05:52:59 +0100 (BST) X-Received: from host ([38.26.242.57]) by pop.metalink.com.br (post.office MTA v2.0 0813 ID# 81-13470) with ESMTP id AAA161; Thu, 1 Jun 2000 01:53:48 -0300 X-To: join29d@hgmp.mrc.ac.uk X-Mailer: Microsoft Outlook Express 4.72.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V(null).1712.3 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk HOW TO SUBSTANTIALLY INCREASE SALES: Easily accept major credit cards right away! ******Act now and all App. & Processing fees waived***** call our (888) 363-7881 now! Our courteous customer care reps. are anxious to help you get your merchant account today. Merchant Status will help you increase sales by an incredible 50% to 400%. Stop losing valuable sales! With one phone call you can be: Accepting all major credit cards! Accepting checks over the net or by =46ax! Accepting real time processing for member sites! Gaining customer loyalty and trust! Close the sale now. No more wondering if "The check is in the mail" We specialize in helping those entrepreneurs whom are just starting out: no credit, poor credit, or even if you have great credit. Almost everyone is approved! =46or the next 5 days we will waive all app. and processing fees! (Other companies charge $200 to $500 to set up) In Business since 1992 Call us today @ 1 (888) 363-7881 and ask for extension =46BK for free setup! **************************************************** If you have received this message in error, please remove at: mailto:qp88k@netscape.net?subject=3Dremove **************************************************** --- From owner-bio-software@hgmp.mrc.ac.uk Thu Jun 1 06:36:55 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5FA9617B01; Thu, 1 Jun 2000 06:36:54 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id BF03917ABA; Thu, 1 Jun 2000 06:36:52 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 25C68415DA for ; Thu, 1 Jun 2000 06:36:52 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id GAA10310 for bio-software-list@hgmp.mrc.ac.uk; Thu, 1 Jun 2000 06:36:51 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "wei" X-Newsgroups: bionet.software Subject: 快報快報 Date: Thu, 1 Jun 2000 13:34:29 +0800 Organization: DCI HiNet Lines: 27 Message-ID: <8h4spf$e2l@netnews.hinet.net> X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk 快報!快報!快報! cf168電子報,一份屬於您的專業網路電子報 cf168電子報每月提撥廣告利潤知80%與訂戶共享,讓您在家看免費電子報,每月還有薪水可拿即日起只要您上網訂閱cf168專業網路電子報,不但不用完全免費,無任何條件),每月還有固定薪水可拿(約台幣 5萬以上),不用抽獎,人人通通有獎訂閱網址:www.cf168.com.tw 因cf168電子報之利潤只限會員共享,且為保障會員權益 ,採會員推薦制,欲入會者需由會員推薦方可入會在此提供下列資料,供有興趣者訂閱用推薦人:陳朝威 (推薦者姓名) 您的訂閱編號:18016 (推薦者會員編號5-10碼) 因此站近來極為熱門,若一時間無法登錄,請多試幾次! From owner-bio-software@hgmp.mrc.ac.uk Thu Jun 1 21:17:48 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B4EBB17B41; Thu, 1 Jun 2000 21:17:47 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 9765117B13; Thu, 1 Jun 2000 21:17:46 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 0AEDF415D5 for ; Thu, 1 Jun 2000 21:17:45 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA28759 for bio-software-list@hgmp.mrc.ac.uk; Thu, 1 Jun 2000 21:17:45 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "RichardK" X-Newsgroups: bionet.software Subject: Moderators Wanted Date: Thu, 1 Jun 2000 21:16:39 +0100 Organization: Whey-Hey.com Lines: 8 Message-ID: <8h6gd6$8sf$1@gxsn.com> Reply-To: "RichardK" X-Trace: 959890662 1NNUCNF1GEBCFC393C gxsn.com X-Complaints-To: abuse@gxsn.com X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk ~ Wanted ~ Moderators for new Instant Messanger on a new search engine @ http://www.whey-hey.com To apply simply email: applications@whey-hey.co.uk with your full name, age, location & country. This is a voluntary positon. From owner-bio-software@hgmp.mrc.ac.uk Fri Jun 2 15:37:13 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9238A17A9B; Fri, 2 Jun 2000 15:37:12 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 40D3917AA1; Fri, 2 Jun 2000 15:37:10 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 736EE415CA for ; Fri, 2 Jun 2000 15:37:09 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA12551 for bio-software-list@hgmp.mrc.ac.uk; Fri, 2 Jun 2000 15:37:08 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Simon Lin" X-Newsgroups: bionet.software Subject: HMMER w/ GCG db? Date: Fri, 2 Jun 2000 10:35:26 -0400 Organization: Duke University, Durham, NC, USA Lines: 9 Message-ID: <8h8gqh$hv0$1@news.duke.edu> X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2919.6600 X-Mimeole: Produced By Microsoft MimeOLE V5.00.2919.6600 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hello, Anybody has experience of using GCG databases with HMMER? Thanks! Simon From owner-bio-software@hgmp.mrc.ac.uk Fri Jun 2 19:30:29 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4913B17B16; Fri, 2 Jun 2000 19:30:29 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id CBB0F17B04; Fri, 2 Jun 2000 19:30:27 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4579F415D4 for ; Fri, 2 Jun 2000 19:30:27 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA15436 for bio-software-list@hgmp.mrc.ac.uk; Fri, 2 Jun 2000 19:30:26 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: ympiceno@my-deja.com X-Newsgroups: bionet.software Subject: software advise requested for off-line searches Date: Fri, 02 Jun 2000 18:18:38 GMT Organization: Deja.com - Before you buy. Lines: 20 Message-ID: <8h8tpv$ii9$1@nnrp2.deja.com> X-Trace: nnrp2.deja.com 959969919 19017 10.12.1.135 (2 Jun 2000 18:18:39 GMT) X-Complaints-To: usenet@deja.com X-Article-Creation-Date: Fri Jun 02 18:02:06 2000 GMT X-Http-User-Agent: Mozilla/4.0 (compatible; MSIE 5.0; Windows 98; DigExt) X-Http-Proxy: 1.1 x58.deja.com:80 (Squid/1.1.22) for client 172.137.212.136 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hello, A co-wroker and I are trying to decide on software packages that wuldbest suit our needs. Firstly, we need to be able to search large phylogenetic databases (e.g. GenBank) off-line. Secondly, we would like to do multilpe alignments, build trees, and one a different note, analyze gel patterns. BioNumerics has a great package that covers almost all of this, but it is very costly. Are there easy to learn, good packages available that you recommend? We use PCs (i.e. no Macs, Unix, or Linux systems). Many Thanks, Yvette Piceno (ympiceno@aol.com) Sent via Deja.com http://www.deja.com/ Before you buy. From owner-bio-software@hgmp.mrc.ac.uk Sat Jun 3 08:16:13 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7430B17B00; Sat, 3 Jun 2000 08:16:13 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 4154317ABE; Sat, 3 Jun 2000 08:16:12 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 69606415DC for ; Sat, 3 Jun 2000 08:16:11 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA03076 for bio-software-list@hgmp.mrc.ac.uk; Sat, 3 Jun 2000 08:16:11 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: adangs@netease.com ("truename") X-Newsgroups: bionet.software Subject: help Date: 3 Jun 2000 08:16:10 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 10 Message-ID: <3938B16D.26026@freemail2.netease.com> Mime-Version: 1.0 X-Trace: niobium.hgmp.mrc.ac.uk 960016570 3073 193.62.192.80 (3 Jun 2000 07:16:10 GMT) X-Complaints-To: news@net.bio.net X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id DE7CD17ABE; Sat, 3 Jun 2000 08:16:08 +0100 (BST) X-Received: from mx1.netease.com (unknown [202.103.134.9]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 04DC6415DC for ; Sat, 3 Jun 2000 08:15:55 +0100 (BST) X-Received: by mx1.netease.com (Postfix, from userid 60001) id 904A71CAB02C4; Sat, 3 Jun 2000 15:19:09 +0800 (CST) X-To: bio-soft@net.bio.net X-Priority: 3 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk liyudong2000@163.net help ___________________________________________________________________ 21CN(www.21cn.com)迵厙眢(www.163.com)僕肮盓厥CNNIC覃脤ㄛワ善CNNIC芘21CN珨⑺ㄛワ芘厙眢珨⑺ㄐ http://fsurvey.cnnic.net.cn/survey/index.html --- From owner-bio-software@hgmp.mrc.ac.uk Sun Jun 4 19:31:09 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E117117B44; Sun, 4 Jun 2000 19:31:08 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A5C3017A99; Sun, 4 Jun 2000 19:31:07 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id EA6B1415D5 for ; Sun, 4 Jun 2000 19:31:06 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA06503 for bio-software-list@hgmp.mrc.ac.uk; Sun, 4 Jun 2000 19:31:06 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Carolin Papp" X-Newsgroups: bionet.software Subject: Has anybody the getright4.2 code ? Date: Fri, 2 Jun 2000 15:00:51 +0200 Organization: T-Online Lines: 5 Message-ID: <8he77a$vkb$16$1@news.t-online.com> Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.t-online.com 960143402 16 32395 320068092733-0001 000604 18:30:02 X-Complaints-To: abuse@t-online.de X-Sender: 320068092733-0001@t-dialin.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi, recently I had download getright4.2 but I dont want to buy it , so I惴 looking for the code. Can anybody help me ? From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 5 14:39:09 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8F4CA17AB6; Mon, 5 Jun 2000 14:39:08 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id D453017AAC; Mon, 5 Jun 2000 14:39:05 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 502A9415D5 for ; Mon, 5 Jun 2000 14:39:05 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA28422 for bio-software-list@hgmp.mrc.ac.uk; Mon, 5 Jun 2000 14:39:04 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: nospam@nospam.net X-Newsgroups: bionet.software Subject: Blast search updater under Redhat 6.1? Date: Mon, 05 Jun 2000 09:39:19 -0400 Organization: Ohio State University Lines: 14 Message-ID: <393BAD87.56D60859@nospam.net> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: charm.magnus.acs.ohio-state.edu 960212341 23406 140.254.128.20 (5 Jun 2000 13:39:01 GMT) X-Complaints-To: abuse@osu.edu X-Mailer: Mozilla 4.7 [en] (WinNT; U) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Wondering if anyone else has come across this. Trying to use the University of Victoria BSU perl script using the Redhat 6.1 package and the latest blastcl3. No problem with blastcl3 working. The script seems to make the correct command line, but the index.html file generated fails to list the output html files. It outputs "results not found" when the results are there in the same directory. The path statements I put into the script seem to be correct. The input is found, and the output goes where it's supposed to. All I can think of is that there's some incompatibility issue. Anyone else seen this? Thanks, Mike Holloway holloway-1@medctr.osu.edu From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 5 17:21:10 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C245917AA5; Mon, 5 Jun 2000 17:21:09 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A775A17A77; Mon, 5 Jun 2000 17:21:08 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id EBB96415CA for ; Mon, 5 Jun 2000 17:21:07 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA00598 for bio-software-list@hgmp.mrc.ac.uk; Mon, 5 Jun 2000 17:21:07 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: nospam@our.site X-Newsgroups: bionet.software Subject: PSI-BLAST: no hits in 1st iteration Date: Mon, 05 Jun 2000 17:13:23 +0100 Organization: Imperial Cancer Research Fund Lines: 115 Message-ID: <8hgjka$i4t$1@icrf.news> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk This message has been posted by: Arne Mueller Hi All, I came across a strange problem when running psi-blast: it didn't find any hits in the first iteration (which is the normal gap-Blast step) but then still goes into iteration 2 and finds itself. Do you have any explanation for this? here's my commandline: query is: >90740 MDSAKxxxxxxxxxxxxxxxxxxxxxGTDCIVDxxxxxxxxxxxxxxxxxxxxQD [ off course it's stupid to psi-blast that kind of query - but still it doens't explain the observed behaviour, does it? ] blastpgp -i 90740.seq -d my_db -j 5 -h 0.0005 -e 100.0 -v 0 -b 2000 > 90740.blast and here's the output (the query is part of the protein database I used): BLASTP 2.0.12 [Apr-21-2000] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 90740 (55 letters) Database: /bmm/data/blast/20000509/nrbagpuss 576,299 sequences; 168,862,208 total letters Searching..................................................done ***** No hits found ****** Searching..................................................done Results from round 2 CONVERGED! >90740 query,ref,sp,pir,gb,emb Length = 55 Score = 26.8 bits (55), Expect = 27 Identities = 14/55 (25%), Positives = 14/55 (25%) Query: 1 MDSAKXXXXXXXXXXXXXXXXXXXXXGTDCIVDXXXXXXXXXXXXXXXXXXXXQD 55 MDSAK GTDCIVD QD Sbjct: 1 MDSAKIINIILSLFLPPVAVFLARGWGTDCIVDIILTILAWFPGMLYALYIVLQD 55 Database: /bmm/data/blast/20000509/nrbagpuss Posted date: Jun 2, 2000 7:42 PM Number of letters in database: 168,862,208 Number of sequences in database: 576,299 Lambda K H 0.301 0.0691 0.162 Lambda K H 0.270 0.0242 0.230 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 3318962 Number of Sequences: 576299 Number of extensions: 11215 Number of successful extensions: 1 Number of sequences better than 100.0: 1 Number of HSP's better than 100.0 without gapping: 1 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1 length of query: 55 length of database: 168,862,208 effective HSP length: 34 effective length of query: 21 effective length of database: 149,268,042 effective search space: 3134628882 effective search space used: 3134628882 T: 11 A: 40 X1: 16 ( 6.9 bits) X2: 38 (14.8 bits) X3: 64 (24.9 bits) S1: 42 (22.1 bits) S2: 51 (25.2 bits) thanks a lot for comments ;-) Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)207 2693405 | fax :+44-(0)207-269-3534 email : a.mueller@icrf.icnet.uk | http://www.bmm.icnet.uk From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 5 17:24:25 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 92F9617AE1; Mon, 5 Jun 2000 17:24:24 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C1F3D17AA5; Mon, 5 Jun 2000 17:24:21 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id AD394415CA for ; Mon, 5 Jun 2000 17:24:20 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA00605 for bio-software-list@hgmp.mrc.ac.uk; Mon, 5 Jun 2000 17:24:19 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: nospam@nospam.net X-Newsgroups: bionet.software Subject: Blast/Entrez search updaters? Date: Mon, 05 Jun 2000 12:24:37 -0400 Organization: Ohio State University Lines: 9 Message-ID: <393BD445.2036CF1F@nospam.net> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: charm.magnus.acs.ohio-state.edu 960222258 27141 140.254.128.20 (5 Jun 2000 16:24:18 GMT) X-Complaints-To: abuse@osu.edu X-Mailer: Mozilla 4.7 [en] (WinNT; U) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I was wondering if anyone could comment on automatic database search update tools available. I'm aware of the Doubletwist search agent available to subscribers only, and the BSU perl script that uses blastcl3. Are there other tools of this sort out there somewhere? Thanks, Mike Holloway holloway-1@medctr.osu.edu From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 5 17:48:02 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0676217A77; Mon, 5 Jun 2000 17:48:01 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 5B04B17A60; Mon, 5 Jun 2000 17:48:00 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id AD418415D4 for ; Mon, 5 Jun 2000 17:47:59 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA00836 for bio-software-list@hgmp.mrc.ac.uk; Mon, 5 Jun 2000 17:47:58 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f Message-ID: <393BD983.3C360AB8@ircm.qc.ca> From: Johanne Duhaime Organization: IRCM X-Mailer: Mozilla 4.7 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 X-Newsgroups: bionet.software Subject: Re: Blast/Entrez search updaters? References: <393BD445.2036CF1F@nospam.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 17 Date: Mon, 05 Jun 2000 16:47:56 GMT X-Trace: carnaval.risq.qc.ca 960223676 207.162.51.5 (Mon, 05 Jun 2000 12:47:56 EDT) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk What about dbwatcher? http://www-igbmc.u-strasbg.fr/BioInfo/LocalDoc/DBWatcher/ which also use blastcl3 nospam@nospam.net wrote: > I was wondering if anyone could comment on automatic database search > update tools available. I'm aware of the Doubletwist search agent > available to subscribers only, and the BSU perl script that uses > blastcl3. Are there other tools of this sort out there somewhere? > > Thanks, > Mike Holloway > holloway-1@medctr.osu.edu From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 5 18:51:21 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5F08417A60; Mon, 5 Jun 2000 18:51:20 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 05E1F17A7A; Mon, 5 Jun 2000 18:51:18 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id E8035415DA for ; Mon, 5 Jun 2000 18:51:17 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA01546 for bio-software-list@hgmp.mrc.ac.uk; Mon, 5 Jun 2000 18:51:17 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Chris Shaffer X-Newsgroups: bionet.software Subject: Seeking image software for exact alignment Date: 5 Jun 2000 17:50:25 GMT Organization: Washington University in St. Louis Lines: 25 Message-ID: <8hgp91$5vq$1@newsreader.wustl.edu> X-Trace: newsreader.wustl.edu 960227425 6138 128.252.76.41 (5 Jun 2000 17:50:25 GMT) X-Complaints-To: usenet@newsreader.wustl.edu Summary: seeking image software to "shift" colors User-Agent: tin/pre-1.4-19990216 ("Styrofoam") (UNIX) (SunOS/5.7 (sun4u)) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hello, We recently purchased a new fluorescent microscope with a CCD camera. When capturing images of flourescent beads we have noticed that the FITC and TRITC signals do not align perfectly when the two images are merged together. In order to do precise co-localization experiments we would like to find some software that would take the image files (usually in 8 or 16 bit TIFF) and be able to have the software "shift" the red image with respect to the green image. The software should be able to do this in a precise and exactly repeatable way. The idea is to emperically determine the "shift" with beads and then correct this at the software level on our experimental images. The microscope salesman has some software that will to this but it is $4000. (ouch!) I have tried using Photoshop but the only technique I have had success with involves draging which is neither precise nor repeatable. What I want is to tell the software to "shift" the red plane 2 pixels up and one pixel to the left. If anyone knows how to do this in photoshop or other software that can do this I would be very interested in hearing from you. thanks Chris Shaffer chris@biology.wustl.edu From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 5 19:45:30 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0D46517AE7; Mon, 5 Jun 2000 19:45:29 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 49CE317AEA; Mon, 5 Jun 2000 19:45:27 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 7E112415DA for ; Mon, 5 Jun 2000 19:45:26 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA02282 for bio-software-list@hgmp.mrc.ac.uk; Mon, 5 Jun 2000 19:45:26 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: greg@franklin.burnham-inst.org (Dr. Greg Quinn) X-Newsgroups: bionet.software Subject: Re: Blast search updater under Redhat 6.1? Date: 5 Jun 2000 18:53:29 GMT Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE Lines: 32 Message-ID: <8hgsv9$rni$1@franklin.ljcrf.edu> References: <393BAD87.56D60859@nospam.net> X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I think Chris Upton set up a bulletin board to discuss BSU issues. nospam@nospam.net wrote: : Wondering if anyone else has come across this. Trying to use the : University of Victoria BSU perl script using the Redhat 6.1 package and : the latest blastcl3. No problem with blastcl3 working. The script : seems to make the correct command line, but the index.html file : generated fails to list the output html files. It outputs "results not : found" when the results are there in the same directory. The path : statements I put into the script seem to be correct. The input is : found, and the output goes where it's supposed to. All I can think of : is that there's some incompatibility issue. Anyone else seen this? : : Thanks, : Mike Holloway : holloway-1@medctr.osu.edu : -- ***************************************** Computational Biology Group The Burnham Institute (formerly La Jolla Cancer Research Inst.) 10901 North Torrey Pines road La Jolla CA92037 Phone:(619) 646 3103 Email: greg@franklin.ljcrf.edu http://franklin.ljcrf.edu/greg http://www.greg.com/ ***************************************** From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 5 19:55:07 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id ACEE017AE7; Mon, 5 Jun 2000 19:55:06 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 89FA217A7A; Mon, 5 Jun 2000 19:55:05 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id E3EC4415CA for ; Mon, 5 Jun 2000 19:55:04 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA02398 for bio-software-list@hgmp.mrc.ac.uk; Mon, 5 Jun 2000 19:55:04 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Cornelius Krasel Subject: Re: Seeking image software for exact alignment X-Newsgroups: bionet.software References: <8hgp91$5vq$1@newsreader.wustl.edu> Organization: =?ISO-8859-1?Q?Universit=E4t_W=FCrzburg?= User-Agent: tin/pre-1.4-19990805 ("Preacher Man") (UNIX) (Linux/2.2.13 (i686)) Date: Mon, 5 Jun 2000 20:52:37 +0200 Message-ID: X-Trace: 5 Jun 2000 20:55:01 +0100, wpxx02.toxi.uni-wuerzburg.de Lines: 28 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Chris Shaffer wrote: > I have tried using Photoshop but the only technique I have had success > with involves draging which is neither precise nor repeatable. What I > want is to tell the software to "shift" the red plane 2 pixels up and one > pixel to the left. Photoshop 4.0 on a Mac: Select the red channel (Menu Window --> Show Channels --> click on "red" in appearing window , then Menu Select --> All (or use "apple-A")) Menu Layer --> Transform --> Submenu Numeric A box will appear (you can reach this box also with "shift-apple-T"). The box has four major transformation options: Position, Scale, Skew and Rotate. Deselect everything except "Position". You can choose how many pixels, cm, whatever, you want to move the layer. HTH, --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP4 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 5 20:44:25 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D8C0B17AEA; Mon, 5 Jun 2000 20:44:24 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A01B617AE9; Mon, 5 Jun 2000 20:44:22 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B64C1415CA for ; Mon, 5 Jun 2000 20:44:21 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id UAA02973 for bio-software-list@hgmp.mrc.ac.uk; Mon, 5 Jun 2000 20:44:21 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: mathog@seqaxp.bio.caltech.edu (David Mathog) X-Newsgroups: bionet.software Subject: Re: HMMER w/ GCG db? Date: 5 Jun 2000 19:41:14 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 73 Message-ID: <8hgvoq$obc@gap.cco.caltech.edu> References: <8h8gqh$hv0$1@news.duke.edu> Reply-To: mathog@seqaxp.bio.caltech.edu To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk In article <8h8gqh$hv0$1@news.duke.edu>, "Simon Lin" writes: >Hello, > >Anybody has experience of using GCG databases with HMMER? I've just been working on that recently. This is for OpenVMS, but I suspect what I say will be true for Unix as well. This is also a work in progress, as I still have some bugs to iron out. HMMSEARCH will read a protein database with no problems when I specify it like "sw:swissprot.seq". However, that doesn't get you anywhere if you want to use the equivalent of /infile=gb:* or /infile=@whatever.lis To deal with that I've used our very hacked up local version of TOFASTA in a pipe, to translate the DNA to protein and feed it on the fly into hmmsearch like: $ pipe tofasta/infile=gb_pr*/frames=123456/out=sys$output | - hmmsearch blah.hmm sys$input > results.out 1. I had to modify sqio.c in the hmmer package to treat "sys$input" like "-" on Unix. On unix "hmmsearch blah.hmm - > results.out" should work without any modificatins. 2. There's some sort of memory problem feeding hmmsearch a really large translated database in this manner - I only just today wrote to S. Eddy about that so don't know the solution yet. It may or may not affect Unix systems. I suspect it will cause the hmmsearch process to use a lot of memory though. I also suspect that the problem is related to the huge "protein" fasta entries which result from just translating an entire genbank DNA entry. Since it seems to depend more on the composition of the data fed in than on the absolute size of the database. In order to work around the memory problem this works: $ tofasta/infile=gb_pr*/frames=123456/out=sys$output/scommand="@dohmmsearch %s"/split=300/sfrag="frag" Which chews off 300 entries from the database, translates in all 6 frames, and writes that to a temporary file. The procedure dohmmsearch then picks up the file (the name goes in on the %s), feeds it into hmmsearch as a normal file, and then deletes the temporary file and returns. Tofasta makes the next one, and round and round it goes. This definitely works, but you can't just blindly specify an "E" value because that is proportional to the size of the database. So if you change the "split" value, you also have to change "E" in the dohmmsearch procedure. (I've asked Sean if there's some way to specify the score value as a cutoff, but have not heard back yet.) As I said, our tofasta has been modified, here are the added switches: /FRames=123456 Translate into forward/reverse reading frames creating new entries with names -for1, etc for each /SPlit=N Create a new output file every N input entries /SName="frag" Name to give each fragment (required if /SPLIT) /SCommand="@dothis %s" Command which is run on each fragment written (requires /SPLIT) I suspect I'm going to have to add a switch to cause translated fragments to automatically break into overlapping pieces below some maximum size. Not many programs were written to expect a 100,000 aa protein! Please email me directly if you have more specific questions. Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 5 20:54:19 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4BB6317AEA; Mon, 5 Jun 2000 20:54:19 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C4D8717AE9; Mon, 5 Jun 2000 20:54:17 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 23E12415CA for ; Mon, 5 Jun 2000 20:54:17 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id UAA03087 for bio-software-list@hgmp.mrc.ac.uk; Mon, 5 Jun 2000 20:54:16 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: nospam@nospam.net X-Newsgroups: bionet.software Subject: Re: Blast/Entrez search updaters? Date: Mon, 05 Jun 2000 15:54:34 -0400 Organization: Ohio State University Lines: 20 Message-ID: <393C057A.A6C55E2C@nospam.net> References: <393BD445.2036CF1F@nospam.net> <393BD983.3C360AB8@ircm.qc.ca> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: charm.magnus.acs.ohio-state.edu 960234854 1502 140.254.128.20 (5 Jun 2000 19:54:14 GMT) X-Complaints-To: abuse@osu.edu X-Mailer: Mozilla 4.7 [en] (WinNT; U) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Johanne Duhaime wrote: > What about dbwatcher? > http://www-igbmc.u-strasbg.fr/BioInfo/LocalDoc/DBWatcher/ which also use > blastcl3 Thanks for the suggestion, but please let me know if there's any additional documentation/help available to make the thing work. Maybe I'm just blind or stupid, but I can't find any obvious way of getting this thing to use blastcl3 on a Linux box. The documentation seems to be for a previous version that doesn't have any options for blastcl3, and the Linux executables from Askok Aiyar don't have any documentation. In looking over the DBwatcher docs, and running the Setdbwatcher program from the Linux version, the Linux package seems to be set up for local searchs only. Does one have to recompile using blastcl3 libraries somehow? Thanks, Mike Holloway holloway-1@medctr.osu.edu From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 5 21:23:22 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 524CC17AEA; Mon, 5 Jun 2000 21:23:22 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id DFBB917A5C; Mon, 5 Jun 2000 21:23:20 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 55CC3415D5 for ; Mon, 5 Jun 2000 21:23:20 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA12133 for bio-software-list@hgmp.mrc.ac.uk; Mon, 5 Jun 2000 21:23:20 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: nospam@nospam.net X-Newsgroups: bionet.software Subject: Re: Blast search updater under Redhat 6.1? Date: Mon, 05 Jun 2000 16:23:36 -0400 Organization: Ohio State University Lines: 13 Message-ID: <393C0C48.C1D5DBE@nospam.net> References: <393BAD87.56D60859@nospam.net> <8hgsv9$rni$1@franklin.ljcrf.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: charm.magnus.acs.ohio-state.edu 960236596 2217 140.254.128.20 (5 Jun 2000 20:23:16 GMT) X-Complaints-To: abuse@osu.edu X-Mailer: Mozilla 4.7 [en] (WinNT; U) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk "Dr. Greg Quinn" wrote: > I think Chris Upton set up a bulletin board to discuss BSU issues. Thanks, but I can't find any mention of this at his site (http://athena.bioc.uvic.ca/genomes/#BSU), or in the docs, just registration for update information. If anyone knows of other information sources for BSU, please let me know. Thanks, Mike Holloway holloway-1@medctr.osu.edu From owner-bio-software@hgmp.mrc.ac.uk Tue Jun 6 01:44:30 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 11CA017AEC; Tue, 6 Jun 2000 01:44:29 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 2ABDD17A5B; Tue, 6 Jun 2000 01:44:28 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A5500415CA for ; Tue, 6 Jun 2000 01:44:27 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id BAA15218 for bio-software-list@hgmp.mrc.ac.uk; Tue, 6 Jun 2000 01:44:27 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Jennifer_Pan@brown.edu X-Newsgroups: bionet.software Subject: software for intron/exon publishing Date: 6 Jun 2000 01:44:26 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 24 Message-ID: <393C49C0.A86475D4@brown.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 960252266 15215 193.62.192.80 (6 Jun 2000 00:44:26 GMT) X-Complaints-To: news@net.bio.net X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 4703817A5B; Tue, 6 Jun 2000 01:44:24 +0100 (BST) X-Received: from vega.brown.edu (vega-22.services.brown.edu [128.148.22.79]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2707A415CA for ; Tue, 6 Jun 2000 01:44:23 +0100 (BST) X-Received: from brown.edu ([128.148.153.121]) by vega.brown.edu (8.9.3/8.9.3) with ESMTP id UAA03535; Mon, 5 Jun 2000 20:44:21 -0400 (EDT) X-Mailer: Mozilla 4.61 [en] (Win95; I) X-Accept-Language: en X-To: bio-software@net.bio.net To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi, I am looking for a free software which can help me making a map of a gene exon1 exon2 |-----| |---| --------|-----|--------------------------------|---|--------------------------- et al where the linear sizes of the introns and exons are proportional to the actual bp length of the gene Does anyone know if such a software is available. It doesn;t seem to be so hard a task at all, I think. It might hide in some of the programs that I have looked at. Any input is appreciated. thanks Jennifer Pan Jennifer_Pan@brown.edu --- From owner-bio-software@hgmp.mrc.ac.uk Tue Jun 6 08:17:09 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 19C3417ACB; Tue, 6 Jun 2000 08:17:09 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id ACA7F17A87; Tue, 6 Jun 2000 08:17:07 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id F0EAC415CA for ; Tue, 6 Jun 2000 08:17:06 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA19786 for bio-software-list@hgmp.mrc.ac.uk; Tue, 6 Jun 2000 08:17:06 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: curiouser@ccmb.ap.nic.in ("Malay") X-Newsgroups: bionet.software Subject: Sequence analysis using Web Resources, SeWeR version 2.0 Date: 6 Jun 2000 08:17:05 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 77 Message-ID: <001601bfcf87$13823c20$7b02a8c0@nic.in> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 960275825 19783 193.62.192.80 (6 Jun 2000 07:17:05 GMT) X-Complaints-To: news@net.bio.net X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id B8A3C17A87; Tue, 6 Jun 2000 08:17:03 +0100 (BST) X-Received: from gene.ccmbindia.org (unknown [202.54.67.53]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1068A415D4 for ; Tue, 6 Jun 2000 08:15:59 +0100 (BST) X-Received: from w108a.nic.in ([192.168.2.123]) by gene.ccmbindia.org (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id MAA33665 for ; Tue, 6 Jun 2000 12:47:39 -0700 (PDT) X-To: "Bio_soft" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Subject: Sequence analysis using Web Resources, SeWeR version 2.0 http://iubio.bio.indiana.edu/webapps/SeWeR/ http://www.bioinformatics.org/sewer/ http://www.crosswinds.net/~boolda/sewer.htm Dear Netters: SeWeR has come to a stage of general use. And therefore this mail. What is SeWeR? ----------------------- SeWeR is an integrated portal of commonly used bioinformatics services on WWW. What it offers? -------------------- It integrates all the services together seamlessly. Unlike other search launchers it gives you all the options of a particular service and a facility to customize each search for you. Why is SeWeR novel? ----------------------------- # SeWeR is completely server independent. That means you can download SeWeR and can run from your computer. It can even be hosted on Intranet site. # SeWeR is light-weight, the whole package is just ~200k. It can even run from a floppy disk # SeWeR is customizable. Each search can be customized by your choice. SeWeR generates a page customized with your option already filled in. # Bookmarklets: SeWeR offers two bookmarklets, one for PubMed and one for GenBank accession retrieval. These becomes a part of your browser. What are the requirements to use SeWeR? --------------------------------------------------------- Just Netscape 4 or Internet Explorer 4 or higher. A Netscape 6 version is underway. SeWeR runs on any platform, MAC/PC/Unix/Linux where a version 4 browser is available. How do you use SeWeR? ---------------------------------- You can use SeWeR on WWW by using any of the above mentioned sites. Or you can download SeWeR from ftp://iubio.bio.indiana.edu/molbio/analyze/sewer.zip Download the archive. Unzip it. And start sewer.htm in your browser. Other features...? ----------------------- SeWeR gives you search facility to Bionetbook and links to other resources. It is released under GNU general public license, it is free and can be used, modified and hosted freely. Umm... it's *GIF FREE* What is the other requirement to use SeWeR? ------------------------------------------------------------- Best wishes for me... :-) Malay Kumar Basu Centre for Cellular and Molecular Biology Hyderabad 500007 I N D I A Fax: (00-91)40-7171195 Phone: (00-91)40-7172241 ----- Call my cat?! No, I just run the can opener... ----- curiouser@ccmb.ap.nic.in --- From owner-bio-software@hgmp.mrc.ac.uk Tue Jun 6 21:30:24 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B4B8317A9D; Tue, 6 Jun 2000 21:30:23 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 5100717AA3; Tue, 6 Jun 2000 21:30:21 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 95568415D5 for ; Tue, 6 Jun 2000 21:30:20 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA08352 for bio-software-list@hgmp.mrc.ac.uk; Tue, 6 Jun 2000 21:30:20 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "weenie@" , biozentrum.uni-wuerzburg.de@hgmp.mrc.ac.uk (Werner Wolz) X-Newsgroups: bionet.software Subject: Re: software for intron/exon publishing Date: Tue, 06 Jun 2000 20:31:22 GMT Message-ID: <393d5725.19867097@news.informatik.uni-wuerzburg.de> References: <393C49C0.A86475D4@brown.edu> X-Newsreader: Forte Free Agent 1.21/32.243 X-Trace: 6 Jun 2000 22:30:16 +0100, wbzd73.biozentrum.uni-wuerzburg.de Organization: Universitaet Wuerzburg Lines: 51 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi Jennifer, Have a look at the Vector NTI Viewer (download for free at: http://www.informaxinc.com/free/viewer.html). This viewer draws a graphical representation of a sequence, with features (exons, introns, restriction sites etc.) shown as arrows and boxes. The sequence and features are drawn to scale. For further refinement it is possible to import the map in CorelDraw as vector graphics. The viewer can load EMBL-, FASTA-, and GenBank files. The features must have GenBank format and can be produced with Sequin from NCBI for example (if you plan a GenBank submission, you can use Sequin for the preparation of your sequence too). Good Luck, Werner. On 6 Jun 2000 01:44:26 +0100, Jennifer_Pan@brown.edu wrote: > >Hi, I am looking for a free software which can help me making a map of a >gene > exon1 exon2 > |-----| |---| > >--------|-----|--------------------------------|---|--------------------------- >et al > >where the linear sizes of the introns and exons are proportional to the >actual bp length of the gene > >Does anyone know if such a software is available. It doesn;t seem to be >so hard a task at all, I think. >It might hide in some of the programs that I have looked at. Any input >is appreciated. > >thanks > >Jennifer Pan >Jennifer_Pan@brown.edu > > >--- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Werner Wolz, PhD Institute of Human Genetics Biocenter Wuerzburg/Germany %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From owner-bio-software@hgmp.mrc.ac.uk Tue Jun 6 21:45:14 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4B37617B19; Tue, 6 Jun 2000 21:45:12 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 0A65817A9D; Tue, 6 Jun 2000 21:45:09 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 64532415CA for ; Tue, 6 Jun 2000 21:45:09 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA08473 for bio-software-list@hgmp.mrc.ac.uk; Tue, 6 Jun 2000 21:45:08 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Bernd Wollscheid X-Newsgroups: bionet.software Subject: Boxit-Database for Molecular Biology Laboratories Date: Tue, 06 Jun 2000 22:28:19 +0100 Organization: Rechenzentrum der Universitaet Freiburg, Germany Lines: 128 Message-ID: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="MS_Mac_OE_3043175299_16508538_MIME_Part" User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --MS_Mac_OE_3043175299_16508538_MIME_Part Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: 8bit http://www.boxit-labstorage.de/ To all Labscientists, � Did someone recently leave your lab? � Can愒 find things anymore? � Have you lost the information about the contents of a tube or where it is stored? � Are you sick of spending time searching in folders and labbooks or at -20蚓 for a plasmid? � Are you and your co-workers wasting time and money to recreate what you can靖 find anymore? � Change it ! Boxit is an easy to use FileMaker Pro relational database that helps collect, store and organize information about all your antibodies, cells, oligos, plasmids/hosts and other biological samples. No more guesswork for you and your co-workers about how to use your molecular biology tools. Simply store the information you gathered about your biological sample and where you stored the tubes in the provided templates. You should not rely only on your labbook, memory or that somebody who 趾nows� the information will still be around. A simple and short database search will bring the information right to your fingertips in a compact printable format without wasting time and money. A database for labprotocols and a database to order labsupplies, allowing you to control costs, are also included to organize your lab even better. Boxit was successfully tested in several laboratories of the Max-Planck-Institute for Immunobiology in Freiburg, Germany. Get more information on Boxit and download your free trialversion of at: http://www.boxit-labstorage.de/ 咕ernd Wollscheid boxit@kagi.com --MS_Mac_OE_3043175299_16508538_MIME_Part Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Boxit-Database for Molecular Biology Laboratories http://www.boxit-labstorage.de/

To all Labscientists,

=80 Did someone recently leave your lab?

=80 Can=B4t find things anymore?

=80 Have you lost the information about the contents of a tube or where it is= stored?

=80 Are you sick of spending time searching in folders and labbooks or at -20= =B0C for a plasmid?

=80 Are you and your co-workers wasting time and money to recreate what you c= an=B9t find anymore?

=80 Change it !

Boxit is an easy to use FileMaker Pro relational database that helps= collect, store and organize
information about all your antibodies, cells, oligos, plasmids/hosts= and other biological samples.

No more guesswork for you and your co-workers about how to use your molecul= ar biology tools. Simply
store the information you gathered about your biological sample and where y= ou stored the tubes in the
provided templates.

You should not rely only on your labbook, memory or that somebody who =B3know= s=B2 the information will still
be around. A simple and short database search will bring the information ri= ght to your fingertips in a compact
printable format without wasting time and money.

A database for labprotocols and a database to order labsupplies, allowing y= ou to control costs, are also
included to organize your lab even better.

Boxit was successfully tested in several laboratories of the Max-Planck-Ins= titute for Immunobiology in
Freiburg, Germany.

Get more information on Boxit and download your free trialversion of at:
http://www.boxit-labstorage.de/

=A9Bernd Wollscheid boxit@kagi.com

--MS_Mac_OE_3043175299_16508538_MIME_Part-- From owner-bio-software@hgmp.mrc.ac.uk Wed Jun 7 07:26:06 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id DF21917AE3; Wed, 7 Jun 2000 07:26:05 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 0C80717AAF; Wed, 7 Jun 2000 07:26:03 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 66DAD415CA for ; Wed, 7 Jun 2000 07:26:03 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA15380 for bio-software-list@hgmp.mrc.ac.uk; Wed, 7 Jun 2000 07:26:03 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: 3545545@cnnic.com X-Newsgroups: bionet.software Subject: The Internet Spy Guide! Find Out Info on Anyone! Date: 7 Jun 2000 07:26:01 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 168 Message-ID: <200006070623.BAA0000012631@apollo.unomaha.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=unknown-8bit X-Trace: niobium.hgmp.mrc.ac.uk 960359162 15377 193.62.192.80 (7 Jun 2000 06:26:02 GMT) X-Complaints-To: news@net.bio.net X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 6188017AAF; Wed, 7 Jun 2000 07:25:59 +0100 (BST) X-Received: from apollo.unomaha.edu (apollo.unomaha.edu [137.48.1.12]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C2FD9415CA for ; Wed, 7 Jun 2000 07:25:57 +0100 (BST) X-Received: by apollo.unomaha.edu id BAA0000012631; Wed, 7 Jun 2000 01:23:28 -0500 (CDT) X-To: jenny@muaiaics.com To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk READY TO KNOW: CONFEDENTIAL: The SOFTWARE they want BANNED in all 50 STATES. WHY? Because these secrets were never intended to reach your eyes...Get FACTS on ANYONE using the internet!!! Locate Missing Persons, find Lost Relatives, obtain Adresses and Phone Numbers of old school friends, even Skip Trace Dead Beat Spouses. This is not a Private Investigator, but a sophisticated SOFTWARE program DESIGNED to automatically CRACK YOUR CASE with links to thousands of Public Record Databases. Find out SECRETS about your relatives, friends, enemies, and everyone else!--even your Spouse! With the New: INTERNET SPY AND YOU It's absolutely astounding! Here's what you can learn: Liscense Plate Number! Get anyones name and address with just a liscense plate number! (Find that girl you met in traffic!!!) Driving Record! Get anyones driving record! Social security number! Trace anyone by social security number! Address! Get anyone's address with just a name! Unlisted phone numbers! Get anyone's phone number with just a name-even unlisted numbers! Locate! Long lost friends, relatives, a past lover who broke your heart! E-mail! Send anonymous e-mail completely untraceable! Dirty secrets! Discover dirty secrets your in-laws don't want you to know! Investigate anyone! Use the sources that private investigators use (all on the Internet) secretly! Ex-spouse! Learn how to get information on an ex-spouse that will help you win in court! (Dig up old skeletons) Criminal search-Backround check! Find out about your daughters boyfriend! (or her husband) Find out! If you are being investigated! Neighbors! Learn all about your mysterious neighbors! Find out what they have to hide! People you work with! Be astonished by what you'll learn about people you work with! Education verification! Did he really graduate college? Find out! Internet Spy and You Software will help you discover ANYTHING about anyone, with clickable hyperlinks and no typing in Internet addresses! Just insert the floppy disk and Go! You will be shocked and amazed by the secrets that can be discovered about absolutely everyone! Find out the secrets they don't want you to know! About others, about yourself! It's INCREDIBLE what you can find out using Internet Spy and You and the Internet! You'll be riveted to your computer screen! Get the software they're trying to ban! Before it's too late! LIMITED TIME OFFER: ORDER TODAY! Only $24.95 US Check or Money Order We will RUSH YOU our Internet Spy and You software so you can begin discovering all the secrets you ever wanted to know! You can know EVERYTHING about ANYONE with our Internet Spy and You Software. Works with all browsers and all versions of AOL! ATTENTION ORDERS OUTSIDE THE US: You must ad $5 for shipping. Foreign money orders must be payable on a US BANK AND IN US FUNDS! NO EXCEPTIONS! ORDER TODAY: SEND ONLY $24.95 Check or Money Order (you may also send one of your own address labels for accuracy if you have one.) If not Please write clearly and include a valid email address for conformation DON'T WAIT TO GET STARTED... it's as easy as 1. 2. 3. 4. STEP 1 - Print the order form text below or print clearly on a sheet of paper STEP 2 - Type or print your order information into the order form section STEP 3 - Mail order form and payment to the address below. Make all check or money orders payable to Jumpstart! STEP 4 - Include Valid Email Address for Immediate delivery! For Credit Card Orders Fill out this form and mail in along with credit card number/credit card type/experation date Please print the name on the card clearly. Mail the portion below Jumpstart 1348 Washington Avenue #250 Miami Beach, FL. 33139 Mail-in Order Form Name: ______________________________ > > > > > > Address: _____________________________ > > > > > > City/State/Zip___________________________________________ > > > > > > Email Address:____________________________________ end of form DISCLAIMER: The seller of this powerful software resource will not be held responsible for how the purchaser chooses to use its resources. To be removed from our mailing list please send an email to ldavidson2@dcemail.com please put remove in the subject line. Thank you, and Kind Regards, Jumpstart --- From owner-bio-software@hgmp.mrc.ac.uk Wed Jun 7 09:43:47 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id CF0AB17B5C; Wed, 7 Jun 2000 09:43:45 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 2A09617B33; Wed, 7 Jun 2000 09:43:43 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 38183415CA for ; Wed, 7 Jun 2000 09:43:43 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA17033 for bio-software-list@hgmp.mrc.ac.uk; Wed, 7 Jun 2000 09:43:42 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: tosft@ms58.url.com.tw X-Newsgroups: bionet.software Subject: 專業行銷工具--臺灣工商名錄光碟資料庫+400萬筆最新名單 Date: 7 Jun 2000 07:34:43 GMT Organization: tosft Lines: 83 Message-ID: <8hktuj$er3@netnews.hinet.net> To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk 您好: 打擾了 ///6.6/// TSOFT 推薦您~~~ 臺灣工商名錄光碟資料庫提供地址,公司名稱,電話,傳真,企業經理人...等資料百萬多筆資料可查詢.列印報表,郵寄標籤..創造商機!! 使用者介面簡單,輕鬆易用～2000.6.6更新 400萬筆E-mail名單資料庫已經分類並儲存為文字檔 (如ms1.txt ms2.txt ...) 適用於各種發信軟體～2000.6.6更新臺灣工商名錄特色說明： ^^^^^^^^^^^^^^^^^^^^^^ 採光碟收納全省各行各業之公司資料都有，細分縣市地區及行業。視窗中文介面，可依縣市.鄉.鎮.區.街道名做各行各業快速查詢既確實又方便。半年改版一次目前為2000.1月改版版本。計有377個行業別185萬筆資料。可與傳真軟體結合做大量的DM傳真功能強大。每筆資料內含：公司名稱、負責人、地址、電話、傳真(部份缺少)、郵遞區號等。除可做大量傳真外可還列印傳統郵寄名條，及業務訪問報表免除張張手寫省時又方便。本產品資料以政府公報及各種最新市調問卷與廣告回函等，所彙整出的名錄,資料可信度高。絕對讓您在最短的時間內，查到市場中客戶族群的資料為您創造無限的商機及利潤。 E-Mail adress List： ^^^^^^^^^^^^^^^^^^^^ E-Mail為2000.5月最新整理出爐資料名單。含Hinet.seednet... 等各大ISP資料計400萬筆。免費下載發信軟體(目前),未來凡本公司客戶可免費獲得本公司贈送自行研發之全中文介面之e-mail 發送軟體(SMTP/POP3/HTTP/...更強大功能,敬請期待!) 讓您的資料輕鬆確實的呈現在300萬的網路人口面前。　產品價格 ^^^^^^^^ 臺灣工商名錄 (NT500) 400萬筆e-mail名單 (NT$400) 兩套合輯 (NT$700) 訂購單 ================= 訂購產品：姓名：聯絡電話：行動電話：電子郵件：郵遞區號：送貨地址：寄至 tosft@ms58.url.com.tw ================== 訂購需知 ^^^^^^^^ 經網路下單訂購後，貨品隔日寄出，依距離遠近到貨時間大約在3~7天後。本公司定期更新資料，請隨時來信索取最新版本資料。(本版本2000年5月更新) 貨品售出可退換，若有光碟本身損毀無法讀取的狀況，請將產品寄回。 From owner-bio-software@hgmp.mrc.ac.uk Wed Jun 7 10:28:44 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 00B0F17B5B; Wed, 7 Jun 2000 10:28:43 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 26B7117A63; Wed, 7 Jun 2000 10:28:42 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id F2B7C415CA for ; Wed, 7 Jun 2000 10:28:40 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA17833 for bio-software-list@hgmp.mrc.ac.uk; Wed, 7 Jun 2000 10:28:40 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: plewniak@igbmc.u-strasbg.fr (Frederic PLEWNIAK) X-Newsgroups: bionet.software Subject: Re: Blast/Entrez search updaters? Date: Wed, 07 Jun 2000 09:30:46 GMT Organization: CRC - Universite Louis Pasteur Strasbourg France Lines: 25 Message-ID: <393e0c2c.7505753@news.u-strasbg.fr> References: <393BD445.2036CF1F@nospam.net> <393BD983.3C360AB8@ircm.qc.ca> <393C057A.A6C55E2C@nospam.net> X-Trace: news.u-strasbg.fr 960374019 5843 130.79.78.242 (7 Jun 2000 10:33:39 GMT) X-Complaints-To: usenet@u-strasbg.fr X-Newsreader: Forte Free Agent 1.11/32.235 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk No Mike, you're not blind nor stupid. The ability to use blastcl3 with DBWatcher is a recent modification and it is not mentioned in the doc yet, sorry. The Linux executables were built some time ago by Ashok Aiyar and do not implement this modification. You can get the sources for the Blastcl3 DBWatcher version at: ftp://ftp-igbmc.u-strasbg.fr/pub/DBWatcher/dbwatcher_blastcl3.tar.gz I still haven't got any Linux binaries, so you'll have to compile the whole thing. Sorry about that. This modified version is not an actual client of the NCBI Blast server (as the original was) but uses directly the "blastcl3" executable available from the NCBI. Therefore, you don't need the blastcl3 libraries. You don't even need the NCBI toolkit if you don't want to use SetDBWatcher... BTW, it is also able to run "blastall" for local Blast2 searches... I hope this helps, Do not hesitate to contact me if you have any problem. Fred From owner-bio-software@hgmp.mrc.ac.uk Wed Jun 7 12:30:17 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D391417B5F; Wed, 7 Jun 2000 12:30:15 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id CAF7B17B5B; Wed, 7 Jun 2000 12:30:13 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 31DAD415CF for ; Wed, 7 Jun 2000 12:30:13 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id MAA24344 for bio-software-list@hgmp.mrc.ac.uk; Wed, 7 Jun 2000 12:30:12 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: martins@udel.edu X-Newsgroups: bionet.software Subject: Bioinformatics Post-Doc Positions at UDel Date: Wed, 07 Jun 2000 11:17:47 GMT Organization: Deja.com - Before you buy. Lines: 39 Message-ID: <8hlb0h$ocp$1@nnrp1.deja.com> X-Article-Creation-Date: Wed Jun 07 11:17:47 2000 GMT X-Http-User-Agent: Mozilla/4.72 [en] (Win98; U) X-Http-Proxy: 1.0 x57.deja.com:80 (Squid/1.1.22) for client 209.146.91.56 X-MyDeja-Info: XMYDJUIDmartinswellington To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk We anticipate that research positions will be available at appropriate post-doctoral levels at the Delaware Biotechnology Institute (DBI) - a new initiative jointly supported by the State of Delaware, The University of Delaware and an industry consortium. REQUIREMENTS: These positions require a Ph.D. in areas related to Bioinformatics and Computational Science for Biotechnology: including Electrical and Computer Engineering, Computer and Information Science or other related computational science areas with biology interests such as computational biochemistry, computational molecular biology, etc.). Experience in high- performance computing, database management and data mining, computer modeling and visualization techniques is advantageous. DUTIES: Participate, organize and supervise cutting-edge research projects related to bioinformatics; supervise and coordinate the work of graduate students; help in grant proposal preparation and reporting; write technical papers and participate in certain teaching activities in the related fields. CONTACT: Send curriculum vitae and names and contact information of three references to: Dr. Guang R. Gao Professor, Dept. of ECE and DBI University of Delaware Fax (302) 831-4316 Email: ggao@udel.edu SUBMISSION DEADLINE: Until July 15, 2000 MORE INFORMATION: http://www.capsl.udel.edu/CURRENTPROJ/BIOINF/ Sent via Deja.com http://www.deja.com/ Before you buy. From owner-bio-software@hgmp.mrc.ac.uk Wed Jun 7 12:58:51 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8DAEF17B6B; Wed, 7 Jun 2000 12:58:50 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 3CAD517B66; Wed, 7 Jun 2000 12:58:49 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9966F415D5 for ; Wed, 7 Jun 2000 12:58:48 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id MAA24582 for bio-software-list@hgmp.mrc.ac.uk; Wed, 7 Jun 2000 12:58:47 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: mrt3@aol.com X-Newsgroups: bionet.software Subject: 3.95% 30 Yr / 4.95% 40 Yr Mortgages! Date: 7 Jun 2000 12:58:46 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 31 Message-ID: <20000607115843.6A737415DA@mercury.hgmp.mrc.ac.uk> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_018C_01BD9940.715D52A0" X-Trace: niobium.hgmp.mrc.ac.uk 960379127 24580 193.62.192.80 (7 Jun 2000 11:58:47 GMT) X-Complaints-To: news@net.bio.net X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 210DD17B66; Wed, 7 Jun 2000 12:58:45 +0100 (BST) X-Received: from kweb.k-info.fr (unknown [212.155.146.8]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 6A737415DA for ; Wed, 7 Jun 2000 12:58:43 +0100 (BST) X-Received: from [216.77.88.100] by kweb.k-info.fr (Netscape Mail Server v1.1) with SMTP id AAA21324; Wed, 6 Oct 1999 10:04:27 +0200 X-To: lng4@aol.com X-Reply-To: mrt3@aol.com X-Priority: 3 X-MSMailPriority: Normal X-Importance: Normal To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk This is a multi-part message in MIME format. ------=_NextPart_000_018C_01BD9940.715D52A0 Content-Type: text/html; 3.95% 30 Year / 4.95% 40 Year Mortgages Now Available!
Loans from $50,000 to $1,500,000.00.
NO Penalty for early payoff.
Self-Employed and can't show income? NO PROBLEM!!

E-mail DebtFreeHome@aol.com for more information.
Or call Annie Toll-Free at 1-888-826-4859 to Apply!

* In compliance with the proposed legislation for commercial e-mail, (S.1618
#301 (a)(2)(C)) we are providing Contact (debtfreehome@aol.com) and Remove
(constant_removal@yahoo.com) links. Requests sent to the Remove link (and
the Remove link ONLY) will immediately stop further transmissions of this
message at no cost to you.

--- From owner-bio-software@hgmp.mrc.ac.uk Wed Jun 7 17:51:43 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BB8D817B74; Wed, 7 Jun 2000 17:51:42 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id B143A17A53; Wed, 7 Jun 2000 17:51:40 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 3D12C415D4 for ; Wed, 7 Jun 2000 17:51:40 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA29165 for bio-software-list@hgmp.mrc.ac.uk; Wed, 7 Jun 2000 17:51:39 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: aweather@molbiol.ox.ac.uk (Aidan Weatherill) X-Newsgroups: bionet.software Subject: Restriction digest Date: 7 Jun 2000 16:51:36 GMT Organization: Oxford University, England Lines: 9 Message-ID: <8F4CBD8D2FraggleRock1yahoocom@163.1.2.7> X-Trace: news.ox.ac.uk 960396696 22704 163.1.214.87 (7 Jun 2000 16:51:36 GMT) X-Complaints-To: newsmaster@ox.ac.uk User-Agent: Xnews/03.04.11 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I have a long bit of dna sequence, and I want a program that will search for specified restriction sites, and report to me the number and the size distribution of the fragments, anyone know of a sutable program? I dont realy care where they are, I just want to know there distribution. Cheers Aidan From owner-bio-software@hgmp.mrc.ac.uk Wed Jun 7 18:21:03 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 61E7917B86; Wed, 7 Jun 2000 18:21:02 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C6EDB17B72; Wed, 7 Jun 2000 18:21:00 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 27BD1415CF for ; Wed, 7 Jun 2000 18:21:00 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA29436 for bio-software-list@hgmp.mrc.ac.uk; Wed, 7 Jun 2000 18:20:59 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Paraic Kenny X-Newsgroups: bionet.software Subject: Re: Restriction digest Date: Wed, 07 Jun 2000 18:25:04 +0000 Organization: Institute of Cancer Research Lines: 23 Message-ID: <393E937F.9E40FB4B@icr.ac.uk> References: <8F4CBD8D2FraggleRock1yahoocom@163.1.2.7> Reply-To: paraic@icr.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 960398458 29433 193.63.217.241 (7 Jun 2000 17:20:58 GMT) X-Complaints-To: news@net.bio.net X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi Aidan Webcutter is quite a user friendly website, with all the functions (and more) that you need. http://firstmarket.com/cutter/cut2.html Regards Paraic Kenny Aidan Weatherill wrote: > > I have a long bit of dna sequence, and I want a program that will search > for specified restriction sites, and report to me the number and the size > distribution of the fragments, anyone know of a sutable program? > > I dont realy care where they are, I just want to know there distribution. > > Cheers > > Aidan From owner-bio-software@hgmp.mrc.ac.uk Wed Jun 7 18:25:32 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B26C817B5F; Wed, 7 Jun 2000 18:25:31 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 9A44117B33; Wed, 7 Jun 2000 18:25:30 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 18B8F415D5 for ; Wed, 7 Jun 2000 18:25:30 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA29552 for bio-software-list@hgmp.mrc.ac.uk; Wed, 7 Jun 2000 18:25:29 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: cupton@uvic.ca (Chris Upton) X-Newsgroups: bionet.software Subject: Re: Blast search updater under Redhat 6.1? Date: Wed, 07 Jun 2000 10:32:32 -0700 Organization: UVIC Lines: 26 Message-ID: References: <393BAD87.56D60859@nospam.net> <8hgsv9$rni$1@franklin.ljcrf.edu> <393C0C48.C1D5DBE@nospam.net> X-Trace: uvaix7e1.comp.UVic.CA 960398724 133672 142.104.33.102 (7 Jun 2000 17:25:24 GMT) X-Complaints-To: abuse@UVic.CA To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk In article <393C0C48.C1D5DBE@nospam.net>, nospam@nospam.net wrote: > "Dr. Greg Quinn" wrote: > > > I think Chris Upton set up a bulletin board to discuss BSU issues. > > Thanks, but I can't find any mention of this at his site > (http://athena.bioc.uvic.ca/genomes/#BSU), or in the docs, just registration > for update information. If anyone knows of other information sources for > BSU, please let me know. > > Thanks, > Mike Holloway > holloway-1@medctr.osu.edu Hi, If you want to email me directly and include the parts of the script you changed to fit your own system, we can take a look at it and see if we can sort out the problem. Cheers, Chris -- Dept Biochemistry and Microbiology University of Victoria Victoria BC From owner-bio-software@hgmp.mrc.ac.uk Wed Jun 7 22:49:50 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5D79117AB2; Wed, 7 Jun 2000 22:49:50 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 1A01317AAD; Wed, 7 Jun 2000 22:49:49 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8AA3C415DA for ; Wed, 7 Jun 2000 22:49:48 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA11188 for bio-software-list@hgmp.mrc.ac.uk; Wed, 7 Jun 2000 22:49:47 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: karplus@cse.ucsc.edu (Kevin Karplus) X-Newsgroups: bionet.software Subject: Re: HMMER w/ GCG db? Date: 7 Jun 2000 21:49:41 GMT Organization: UC Santa Cruz CS/CE Lines: 34 Message-ID: <8hmg1l$g4l@darkstar.ucsc.edu> References: <8h8gqh$hv0$1@news.duke.edu> <8hgvoq$obc@gap.cco.caltech.edu> X-Newsreader: xrn 9.00 Originator: karplus@cse.ucsc.edu To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk In article <8hgvoq$obc@gap.cco.caltech.edu>, mathog@seqaxp.bio.caltech.edu (David Mathog) writes: |> 2. There's some sort of memory problem feeding hmmsearch a really |> large translated database in this manner - I only just today wrote to S. Eddy |> about that so don't know the solution yet. It may or may not affect |> Unix systems. I suspect it will cause the hmmsearch process to use a |> lot of memory though. I also suspect that the problem is related to |> the huge "protein" fasta entries which result from just translating |> an entire genbank DNA entry. Since it seems to depend more on the |> composition of the data fed in than on the absolute size of the |> database. The SAM package provides many of the same features as the HMMer package (and a number of features not available with HMM). We have had no problem with SAM running large databases through the search programs, probably because SAM uses a space-efficient version of the fundamental dynamic programming algorithms. SAM is free to academics and non-profits and is available at reasonable license fees to corporations. See http://www.cse.ucsc.edu/research/compbio/sam.html for more information. You can also try out some of the uses of SAM for free at http://www.cse.ucsc.edu/research/compbio/HMM-apps/HMM-applications.html -- Kevin Karplus karplus@cse.ucsc.edu http://www.cse.ucsc.edu/~karplus life member (LAB, Adventure Cycling, American Youth Hostels) Effective Cycling Instructor #218-ck Anything below this line is junk added by others without my approval. From owner-bio-software@hgmp.mrc.ac.uk Thu Jun 8 07:00:57 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8052717A99; Thu, 8 Jun 2000 07:00:56 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 528A217A8A; Thu, 8 Jun 2000 07:00:55 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id BA74E415CF for ; Thu, 8 Jun 2000 07:00:54 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA17050 for bio-software-list@hgmp.mrc.ac.uk; Thu, 8 Jun 2000 07:00:54 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Andrea Hansen X-Newsgroups: bionet.software Subject: Re: Restriction digest Date: 08 Jun 2000 08:00:49 +0200 Lines: 17 Message-ID: References: <8F4CBD8D2FraggleRock1yahoocom@163.1.2.7> X-Trace: fu-berlin.de 960444052 3633328 134.99.202.44 (16 [4974]) X-Newsreader: Gnus v5.5/XEmacs 20.4 - "Emerald" To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi Aidan, try TACG: http://bioweb.pasteur.fr/seqanal/interfaces/tacg.html or Restriction Enzyme Analysis http://darwin.bio.geneseo.edu/%7Eyin/WebGene/RE.html Andrea aweather@molbiol.ox.ac.uk (Aidan Weatherill) writes: > I have a long bit of dna sequence, and I want a program that will search > for specified restriction sites, and report to me the number and the size > distribution of the fragments, anyone know of a sutable program? -- Institut fuer Botanik III Tel +49 211 81 12339 Heinrich-Heine-Universitaet Fax +49 211 81 13554 Universitaetsstr.1 email : webmaster@bioinformatik.de 40225 Duesseldorf http://www.bioinformatik.de From owner-bio-software@hgmp.mrc.ac.uk Thu Jun 8 14:07:27 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id AD02417ABB; Thu, 8 Jun 2000 14:07:26 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id B668517A53; Thu, 8 Jun 2000 14:07:24 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C9290415D5 for ; Thu, 8 Jun 2000 14:07:23 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA22386 for bio-software-list@hgmp.mrc.ac.uk; Thu, 8 Jun 2000 14:07:23 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Julie THOMPSON-MAALOUM X-Newsgroups: bionet.software Subject: clustalw/x 1.81 release Date: Thu, 08 Jun 2000 14:58:15 +0200 Organization: IGBMC Lines: 78 Message-ID: <393F9867.72F13639@titus.u-strasbg.fr> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.u-strasbg.fr 960473459 15721 130.79.79.210 (8 Jun 2000 14:10:59 GMT) X-Complaints-To: usenet@u-strasbg.fr X-Mailer: Mozilla 4.5 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Clustal W, Clustal X (Version 1.81) 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. This release includes a number of bug fixes for ClustalX, plus the ability to write alignments and phylogenetic trees in Nexus format. The Nexus format provides compatability with several popular phylogeny programs, including PAUP and MacClade. The main changes since Version 1.8 are: - Alignments can now be saved in Nexus format, for compatibility with PAUP, MacClade etc. Phylogenetic trees can also be saved in nexus format. - A bug causing ClustalX to crash during cut-and-paste operations has been fixed. - A bug on PC systems, causing an error message when writing to files with space characters in the filename has been fixed. - The Quality Curve is now displayed as a bar chart, instead of a line plot. - A ClustalX icon has been added for MAC and PC systems. - ClustalW/X now returns error codes for some common errors when exiting. This may be useful for people who run clustalx automatically from within a script. 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 1.81 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@logidee.com) 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 1.81 of Clustal W/X should contact the authors unless they have previously taken out a licence. ****************************************************************************** From owner-bio-software@hgmp.mrc.ac.uk Thu Jun 8 14:12:44 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D867117B4A; Thu, 8 Jun 2000 14:12:43 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 8933417B2B; Thu, 8 Jun 2000 14:12:42 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id CB8DE415CF for ; Thu, 8 Jun 2000 14:12:41 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA22392 for bio-software-list@hgmp.mrc.ac.uk; Thu, 8 Jun 2000 14:12:41 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Fraggle_Rock_1@yahoo.com (Fraggle_Rock) X-Newsgroups: bionet.software Subject: Re: Restriction digest Date: 8 Jun 2000 13:12:35 GMT Organization: Oxford University, England Lines: 21 Message-ID: <8F4D90DA2FraggleRock1yahoocom@163.1.2.7> References: <8F4CBD8D2FraggleRock1yahoocom@163.1.2.7> X-Trace: news.ox.ac.uk 960469955 2546 163.1.214.87 (8 Jun 2000 13:12:35 GMT) X-Complaints-To: newsmaster@ox.ac.uk User-Agent: Xnews/03.04.11 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk aweather@molbiol.ox.ac.uk (Aidan Weatherill) wrote in <8F4CBD8D2FraggleRock1yahoocom@163.1.2.7>: >I have a long bit of dna sequence, and I want a program that will search >for specified restriction sites, and report to me the number and the size >distribution of the fragments, anyone know of a sutable program? > >I dont realy care where they are, I just want to know there distribution. > >Cheers > >Aidan Thanks for the replys so far, but I think the fact that the bit of dna I am analysing is 350KB long is throwing these web based programs. Is there a PC Program that will do the same as these online tools? Thanks again Aidan From owner-bio-software@hgmp.mrc.ac.uk Thu Jun 8 17:29:23 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C69F317B8A; Thu, 8 Jun 2000 17:29:22 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 537D317B0E; Thu, 8 Jun 2000 17:29:20 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id BCAFB415D5 for ; Thu, 8 Jun 2000 17:29:19 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA24890 for bio-software-list@hgmp.mrc.ac.uk; Thu, 8 Jun 2000 17:29:19 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Andrea Hansen X-Newsgroups: bionet.software Subject: Re: Restriction digest Date: 08 Jun 2000 18:29:09 +0200 Lines: 18 Message-ID: References: <8F4CBD8D2FraggleRock1yahoocom@163.1.2.7> <8F4D90DA2FraggleRock1yahoocom@163.1.2.7> X-Trace: fu-berlin.de 960481756 3253056 134.99.202.44 (16 [4974]) X-Newsreader: Gnus v5.5/XEmacs 20.4 - "Emerald" To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk > >I have a long bit of dna sequence, and I want a program that will search > >for specified restriction sites, and report to me the number and the size > >distribution of the fragments, anyone know of a sutable program? > Thanks for the replys so far, but I think the fact that the bit of dna I am > analysing is 350KB long is throwing these web based programs. > Is there a PC Program that will do the same as these online tools? Hi Aidan, look at this site http://www.bioinformatik.de/cgi-bin/browse/Catalog/Software/ You will find a lot of software tools for unix, mac and windows. Andrea -- Institut fuer Botanik III Tel +49 211 81 12339 Heinrich-Heine-Universitaet Fax +49 211 81 13554 Universitaetsstr.1 email : webmaster@bioinformatik.de 40225 Duesseldorf http://www.bioinformatik.de From owner-bio-software@hgmp.mrc.ac.uk Fri Jun 9 02:10:08 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1866A17AA1; Fri, 9 Jun 2000 02:10:08 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id D6A3017A7A; Fri, 9 Jun 2000 02:10:06 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id EAA4D415D4 for ; Fri, 9 Jun 2000 02:10:05 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id CAA09609 for bio-software-list@hgmp.mrc.ac.uk; Fri, 9 Jun 2000 02:10:05 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: cupton@uvic.ca (Chris Upton) X-Newsgroups: bionet.software Subject: FAST-ALERT Date: Thu, 08 Jun 2000 18:17:11 -0700 Organization: UVIC Lines: 9 Message-ID: X-Trace: uvaix7e1.comp.UVic.CA 960513002 190274 142.104.33.102 (9 Jun 2000 01:10:02 GMT) X-Complaints-To: abuse@UVic.CA To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk HI, I'm looking for info on FASTALERT. Anyone know if it's still available? Thanks, Chris Upton -- Dept Biochemistry and Microbiology University of Victoria Victoria BC From owner-bio-software@hgmp.mrc.ac.uk Fri Jun 9 07:46:18 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0A75D17AEF; Fri, 9 Jun 2000 07:46:17 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A0B2417AC3; Fri, 9 Jun 2000 07:46:16 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A85EF415D5 for ; Fri, 9 Jun 2000 07:46:15 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA13498 for bio-software-list@hgmp.mrc.ac.uk; Fri, 9 Jun 2000 07:46:15 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Reinhard Doelz X-Newsgroups: bionet.software Subject: Re: FAST-ALERT Date: Fri, 09 Jun 2000 08:28:55 +0200 Organization: GeneData AG Lines: 13 Message-ID: <39408EA7.ECE24C6D@genedata.com> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.72 [en] (WinNT; U) X-Accept-Language: en To: Chris Upton X-Original-NNTP-Posting-Host: korosi.ch.genedata.com To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk > I'm looking for info on FASTALERT. Anyone know if it's still available? If you refer to Florian Eggenberger's FASTALERT, this was a service of the old Biocomputing Basel facility. Reference: http://www.biozentrum.unibas.ch/~biocomp/report/other/doelz.htm (1995). FASTALERT and the associated HASSLE services are no longer supported. I have at the time of my departure archived the publicly available source code at http://www.doelz.com/software/hassle/ in case you want to have a look at the source code (look at the source with the 'facust' client). Regards Reinhard From owner-bio-software@hgmp.mrc.ac.uk Fri Jun 9 08:56:10 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 65BE017B9C; Fri, 9 Jun 2000 08:56:08 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 1D6D617B9C; Fri, 9 Jun 2000 08:56:05 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 5D316415DA for ; Fri, 9 Jun 2000 08:56:05 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA14343 for bio-software-list@hgmp.mrc.ac.uk; Fri, 9 Jun 2000 08:56:04 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: francis.durst@bota-ulpnospam.u-strasbg.fr (Francis Durst) X-Newsgroups: bionet.software Subject: Re: Restriction digest Date: Fri, 9 Jun 2000 09:56:09 LOCAL Organization: CNRS Lines: 33 Message-ID: References: <8F4CBD8D2FraggleRock1yahoocom@163.1.2.7> <8F4D90DA2FraggleRock1yahoocom@163.1.2.7> X-Trace: news.u-strasbg.fr 960541266 15939 130.79.135.1 (9 Jun 2000 09:01:06 GMT) X-Complaints-To: usenet@u-strasbg.fr X-Newsreader: Trumpet for Windows [Version 1.0 Rev B.7] To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk In article <8F4D90DA2FraggleRock1yahoocom@163.1.2.7> Fraggle_Rock_1@yahoo.com (Fraggle_Rock) writes: >From: Fraggle_Rock_1@yahoo.com (Fraggle_Rock) >Subject: Re: Restriction digest >Date: 8 Jun 2000 13:12:35 GMT >aweather@molbiol.ox.ac.uk (Aidan Weatherill) wrote in ><8F4CBD8D2FraggleRock1yahoocom@163.1.2.7>: >>I have a long bit of dna sequence, and I want a program that will search >>for specified restriction sites, and report to me the number and the size >>distribution of the fragments, anyone know of a sutable program? >> >>I dont realy care where they are, I just want to know there distribution. >> >>Cheers >> >>Aidan >Thanks for the replys so far, but I think the fact that the bit of dna I am >analysing is 350KB long is throwing these web based programs. >Is there a PC Program that will do the same as these online tools? There are several. You may try Generunner which is now free and is found at http://www.generunner.com/ if I remember well, in addition to displaying the usual restriction map + statistics of cutters and non-cutters, it generates fragments from your choice of restriction enzymes. All the best Francis From owner-bio-software@hgmp.mrc.ac.uk Fri Jun 9 09:32:08 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 00FA517AD6; Fri, 9 Jun 2000 09:32:07 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 9F00C17A9E; Fri, 9 Jun 2000 09:32:05 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1D28C415D5 for ; Fri, 9 Jun 2000 09:32:05 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA15362 for bio-software-list@hgmp.mrc.ac.uk; Fri, 9 Jun 2000 09:32:04 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: plewniak@igbmc.u-strasbg.fr (Frederic PLEWNIAK) X-Newsgroups: bionet.software Subject: Re: FAST-ALERT Date: Fri, 09 Jun 2000 08:34:16 GMT Organization: CRC - Universite Louis Pasteur Strasbourg France Lines: 15 Message-ID: <3940abc2.6790634@news.u-strasbg.fr> References: <39408EA7.ECE24C6D@genedata.com> X-Trace: news.u-strasbg.fr 960543426 16596 130.79.78.242 (9 Jun 2000 09:37:06 GMT) X-Complaints-To: usenet@u-strasbg.fr X-Newsreader: Forte Free Agent 1.11/32.235 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk On Fri, 09 Jun 2000 08:28:55 +0200, Reinhard Doelz wrote: >If you refer to Florian Eggenberger's FASTALERT, this was a service of >the old Biocomputing Basel facility. >Reference: >http://www.biozentrum.unibas.ch/~biocomp/report/other/doelz.htm (1995). > The actual reference is: Eggenberger F., Redaschi, N. and Doelz, R.: FastAlert--an automatic search system to alert about new entries in biological sequence databanks. Comput Appl Biosci 12, 129-33(1996). Fred From owner-bio-software@hgmp.mrc.ac.uk Fri Jun 9 15:15:27 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4911317A91; Fri, 9 Jun 2000 15:15:26 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 0253017A8D; Fri, 9 Jun 2000 15:15:24 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 84EC2415D4 for ; Fri, 9 Jun 2000 15:15:24 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA19534 for bio-software-list@hgmp.mrc.ac.uk; Fri, 9 Jun 2000 15:15:24 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: PN X-Newsgroups: bionet.software Subject: NetPrimer does not work??? Date: Fri, 09 Jun 2000 17:09:04 +0300 Organization: University of Oulu Lines: 28 Message-ID: <3940FA7F.FDD71D19@whoccr.oulu.fi_no_spam> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: ousrvr3.oulu.fi 960559733 2832 193.166.38.182 (9 Jun 2000 14:08:53 GMT) X-Complaints-To: news@news.oulu.fi X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi there, Does anybody know why NetPrimer (in http://www.PremierBiosoft.com/netprimer.html) does not work? Or does it work in somebody else's computer? In my case I think that Applet is running because there is a text in the window of Netscape saying "NetPrimerApplet running". The program allows me to type in a sequence and even the light in the analyze button turns on when I type the 10th letter. But when I click the analyze button nothing happens. Did I forget something very simple or is there something strange going on? I also tried it in another PC where I even updated Netscape to 4.73 and program still kept silence. Any ideas? Regards, PN -- If you want to reply, please remove "_no_spam" from my email address. From owner-bio-software@hgmp.mrc.ac.uk Fri Jun 9 18:01:12 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5FE1C17A8B; Fri, 9 Jun 2000 18:01:11 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 9FE3A17A7E; Fri, 9 Jun 2000 18:01:09 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 16C2F415D5 for ; Fri, 9 Jun 2000 18:01:09 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA21474 for bio-software-list@hgmp.mrc.ac.uk; Fri, 9 Jun 2000 18:01:08 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: jakku@mrna.tn.nic.in ("R. Jayakumar") X-Newsgroups: bionet.software Subject: Re: NetPrimer does not work??? Date: 9 Jun 2000 18:01:06 +0100 Organization: School of Biotechnology Lines: 69 Message-ID: <003001bfd234$55a6f280$8c01a8c0@tn.nic.in> References: <3940FA7F.FDD71D19@whoccr.oulu.fi_no_spam> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 960570067 21472 193.62.192.80 (9 Jun 2000 17:01:07 GMT) X-Complaints-To: news@net.bio.net X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 62BA717A7E; Fri, 9 Jun 2000 18:01:05 +0100 (BST) X-Received: from mrna.tn.nic.in (mrna.tn.nic.in [164.100.244.235]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 20EC7415D5 for ; Fri, 9 Jun 2000 18:00:52 +0100 (BST) X-Received: from [192.168.1.140] (helo=vslab.tn.nic.in) by mrna.tn.nic.in with smtp (Exim 3.03 #3) id 130S2b-0000vQ-00; Fri, 09 Jun 2000 22:23:53 +0530 X-Reply-To: "R. Jayakumar" X-To: , "biosoftware on bionet" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk netprimer works very nicely on my PC. Of course, on IE 5.0 and above, it shows a version recognition problem, but the applet runs smoothly. I regularly analyse my primers on it. Probably, you may be missing a few class files or something which does the work of analysis (Java is not my cup of tea, by the way). I will be glad to attach a netprimer as a self extractable file for you if you need mine. bye cheers jayakumar |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||| R. JAYAKUMAR CSIR- Senior Research Fellow Dept. of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai - 625 021. India email: jakku@usaf.org tel: +91-452-858471-374 efax: (603)-688-4665 web: http://members.tripod.com/~jakspage |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||| "There is a possible even in imPOSSIBLE" ----- Original Message ----- From: PN To: Sent: Friday, June 09, 2000 7:39 PM Subject: NetPrimer does not work??? > Hi there, > > Does anybody know why NetPrimer (in > http://www.PremierBiosoft.com/netprimer.html) > does not work? > Or does it work in somebody else's computer? > > In my case I think that Applet is running because there is a text in the > > window of Netscape saying "NetPrimerApplet running". The program allows > me > to type in a sequence and even the light in the analyze button turns on > when > I type the 10th letter. But when I click the analyze button nothing > happens. > Did I forget something very simple or is there something strange going > on? I > also tried it in another PC where I even updated Netscape to 4.73 and > program still kept silence. > Any ideas? > > Regards, > PN > > -- > If you want to reply, please remove "_no_spam" from my email address. > > --- From owner-bio-software@hgmp.mrc.ac.uk Fri Jun 9 18:20:39 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0B9E817B4F; Fri, 9 Jun 2000 18:20:38 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id D754617B4C; Fri, 9 Jun 2000 18:20:37 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C22E0415DA for ; Fri, 9 Jun 2000 18:20:36 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA21721 for bio-software-list@hgmp.mrc.ac.uk; Fri, 9 Jun 2000 18:20:35 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: cupton@uvic.ca (Chris Upton) X-Newsgroups: bionet.software Subject: Re: FAST-ALERT Date: Fri, 09 Jun 2000 10:27:42 -0700 Organization: UVIC Lines: 26 Message-ID: References: <39408EA7.ECE24C6D@genedata.com> <3940abc2.6790634@news.u-strasbg.fr> X-Trace: uvaix7e1.comp.UVic.CA 960571232 138762 142.104.33.102 (9 Jun 2000 17:20:32 GMT) X-Complaints-To: abuse@UVic.CA To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk In article <3940abc2.6790634@news.u-strasbg.fr>, plewniak@igbmc.u-strasbg.fr (Frederic PLEWNIAK) wrote: > On Fri, 09 Jun 2000 08:28:55 +0200, Reinhard Doelz > wrote: > > >If you refer to Florian Eggenberger's FASTALERT, this was a service of > >the old Biocomputing Basel facility. > >Reference: > >http://www.biozentrum.unibas.ch/~biocomp/report/other/doelz.htm (1995). > > > The actual reference is: > Eggenberger F., Redaschi, N. and Doelz, R.: FastAlert--an automatic > search system to alert about new entries in biological sequence > databanks. Comput Appl Biosci 12, 129-33(1996). > > Fred Thanks for the info guys!! Cheers, Chris -- Dept Biochemistry and Microbiology University of Victoria Victoria BC From owner-bio-software@hgmp.mrc.ac.uk Sat Jun 10 19:37:17 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id EBF8917B3F; Sat, 10 Jun 2000 19:37:16 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id CBCA017A56; Sat, 10 Jun 2000 19:37:15 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 0E52D415DD for ; Sat, 10 Jun 2000 19:37:14 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA18859 for bio-software-list@hgmp.mrc.ac.uk; Sat, 10 Jun 2000 19:37:14 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Dong Xu X-Newsgroups: bionet.software Subject: Employment at Oak Ridge National Laboratory Date: Sat, 10 Jun 2000 14:50:14 -0400 Organization: Oak Ridge National Lab, Oak Ridge, TN Lines: 46 Message-ID: <39428DE6.850961B6@ornl.gov> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.02 [en] (X11; I; IRIX 5.3 IP22) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Employment at Oak Ridge National Laboratory Postdoctoral Research Associates and Postmaster Software Engineer Positions in Computational Biology/Bioinformatics Applications are invited for postdoctoral and postmaster positions in the Computational Biosciences Section of Life Sciences Division, at the Oak Ridge National Laboratory. The successful candidates will participate in research and development of computational algorithms and software for mining microarray expression data, modeling biological pathways, or protein structure prediction/modeling. An advanced degree with demonstrated experience in computer programming is required. Additional experience is desired in any of the following areas: bioinformatics, computational biology, biological pathway studies, protein folding/threading, high-performance computing, large-scale software development. Oak Ridge National Laboratory maintains well-equipped facilities; more information on the laboratory and its divisions can be found at: http://www.ornl.gov and http://compbio.lsd.ornl.gov/. Funding is available for appointments of up to three years. They are offered through the ORNL Postdoctoral Research Associates Program and, and the ORNL Postmasters Research Participation Program which are jointly administered by ORNL's Office of University and Science Education and the Oak Ridge Institute for Science and Education. These programs are open to all qualified U.S. and non-U.S. citizens without regard to race, color, age, religion, sex, national origin, physical or mental disability, or status as a Vietnam-era veteran or disabled veteran. Interested candidates should complete and submit a "Recruited Position" application for either the ORNL Postdoctoral Research Associates Program, or the ORNL Postmasters Research Participation Program. An application and a complete description of these programs are available at: http://www.orau.gov/orise/edu/postgrad/ornlpdoc.htm. or http://www.orau.gov/orise/edu/postgrad/ornlpmappmat.htm. A copy of the application can also be obtained by contacting Bonnie DeJarnette at 865-241-5386, or dejarneb@orau.gov. Specific technical questions related to this position should be directed to: Ying Xu, Ph.D., Oak Ridge National Laboratory, PO Box 2008, 1060 Commerce Park Drive, Oak Ridge, TN 37831-6480, 865-574-7263; xyn@ornl.gov. Please reference project #ORNL00-12 when applying for these positions. Applications will be accepted until the positions are filled. From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 12 00:38:15 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 411AE17ACD; Mon, 12 Jun 2000 00:38:15 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id EF12B17AC2; Mon, 12 Jun 2000 00:38:13 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 5544B415DE for ; Mon, 12 Jun 2000 00:38:13 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id AAA26406 for bio-software-list@hgmp.mrc.ac.uk; Mon, 12 Jun 2000 00:38:12 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: 3545545@cnnic.com X-Newsgroups: bionet.software Subject: Powerful Investigative Software! Date: 12 Jun 2000 00:38:11 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 210 Message-ID: <200006112336.BAA28818@pro-s6.pfaffenwinkel.net> Mime-Version: 1.0 Content-Type: text/plain; charset=unknown-8bit X-Trace: niobium.hgmp.mrc.ac.uk 960766692 26403 193.62.192.80 (11 Jun 2000 23:38:12 GMT) X-Complaints-To: news@net.bio.net X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 78B6417AC2; Mon, 12 Jun 2000 00:38:10 +0100 (BST) X-Received: from pro-s6.pfaffenwinkel.net (pro-s6.pfaffenwinkel.net [195.145.198.122]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id EB549415DE; Mon, 12 Jun 2000 00:38:08 +0100 (BST) X-Received: from rac (root@localhost [127.0.0.1]) by pro-s6.pfaffenwinkel.net (8.9.3/8.9.3) with SMTP id BAA28818; Mon, 12 Jun 2000 01:36:22 +0200 X-To: jenny@muaiaics.com To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk We have all heard about the vast amounts of information that an investigator can obtain about an individual. However, did you know that you too can find out practically anything about a person and/or business on your own? Armed with this professional but, easy to use software, you too can use the same sources that private investigators have used for years to track, locate, background check or screen almost anyone. But, you should beware of other detective type products (almost always html or text documents) that claim they will show you how do everything using the net - They simply cover their claims by providing you with links to Information Brokers! Despite the vast amount of information that is available, few states have everything that you might need online. Therefore, our toolkit does not only provide you with a large organized listing of the sites that are available on the net but, also it provides a searchable database of all the offline public government sources that can be found throughout the US! This database contains complete contact information,notes on each source and will even print envelopes addressed to any source that you choose. And, this is just a small fraction of the overall package! Locate People - Find Almost Anyone Lots of information, extensive contact sources and even tools that will allow you to: - Find people who have relocated - Find people who have changed their name or address - Locate resources for adoption related searches - Determine which locate source to use and how - Have the government locate deadbeat parents - Locate people using public records available to anyone - Locate military buddies - Find addresses using just a phone number - Create a map showing directions to a person's house - How to follow the paper trail almost everyone leaves - Use the same tips & tricks that investigator's use when all else fails - Use the post office to determine the address behind a PO Box The toolkit not only provides the sources most useful in locating people but also offers a complete "How To" section that explains how and when to use the different sources and methods provided. This is the software private investigators wish was kept secret! Now at your fingertips! You get all this and MUCH MORE! All for only $24.95 (Shipping & Handling Included!) Tap Into Investigative Sources How and where to investigate, perform or locate: - Credit information - Driver's records - Lawsuit information, civil and criminal - Employment screening - Criminal records - Asset identification - Your own FBI file - Bounty hunter resources - Investigative information - Secrets of someone's past - Find tax liens, property records, vehicle ownership and other public records - Business records - Where to listen in on the police radios (scanner) - Check on doctors, lawyers or other professionals Also within the toolkit is a complete "How To' section devoted on the topic of background investigations. What public sources are available and how you can use them. Search And Make Use Of Various Government Resources Extensive public record sources and Government resources - State by state information and listings to Government provided public records - Searchable Government databases and useful Government publications - CIA, FBI and secret service information - Information on obtaining documents under the FOIA - Legal databases - Court documents Visit Numerous Internet Information Sources Know everything there is to know about the Internet underground and how you can protect yourself - Send anonymous email - Visit illegal drug archives - Track anyone's newsgroup postings - Surf anonymously on the net - Learn how to protect privacy at home and on the net - Check the Internet's better business bureau - Visit illegal software piracy sites - Visit anarchist sites (Loads of information files on just about anything) - Search criminal databases - Visit virus distribution and prevention sites - Search the underground bookstores & gather underground information - Find unusual products and spy related gadgets Unlike most of the rest of the current internet detective programs available, this program does not simply provide you with a text file of resources (usually addresses and phone numbers). Nor is it simply an HTML Document with pretty pictures advertised as "software" but rather it is a powerful WIN95/98 program that provides you with the tools necessary to locate and use the resources available on the internet right from the program! BUILT-IN INVESTIGATIVE DATABASES The toolkit also provides you with investigative databases that you will not find anywhere else including the Information Sources dB (public record sources) and an interface allowing complete access to the private Investigative Sources dB (sources, tips, misc. information) all without additional cost. NOT JUST INFORMATION - MANY TOOLS The CD Toolkit has an option that you can use to create a Cyber-Track & Spy diskette. Armed with this diskette you can track anyone's internet activity. Simply install the secret tracking files from this diskette onto a computer and all URLs visited will be secretly tracked and recorded. Our Search Utility allows you to perform general and investigative type searches over the internet. With one click of a button, one can retrieve general search query results, people's addresses & phone numbers and much more. (The search utility is a small scale version of CD's Cyber-Data Retriever software) You will never have to worry about how old the information is and whether or not it is even valid! Our program is updated approximately every third month and these updates are always free to anyone who has purchased the program via download. This is the software private investigators wish was kept secret! Now at your fingertips! You get all this and MUCH MORE! All for only $24.95 (Shipping & Handling Included!) LIMITED TIME OFFER: ORDER TODAY! Only $24.95 US Check or Money Order We will RUSH YOU your software so you can begin discovering all the secrets you ever wanted to know! You can know EVERYTHING about ANYONE with our Internet Spy and Your Software. Works with all browsers and all versions of AOL! Does not work with WebTV. ATTENTION ORDERS OUTSIDE THE US: You must ad $5 for shipping. Foreign money orders must be payable on a US BANK AND IN US FUNDS! NO EXCEPTIONS! ORDER TODAY: SEND ONLY $24.95 Check or Money Order (you may also send one of your own address labels for accuracy if you have one.) If not Please write clearly and include a valid email address for conformation DON'T WAIT TO GET STARTED... it's as easy as 1. 2. 3. 4. STEP 1 - Print the order form text below or print clearly on a sheet of paper STEP 2 - Type or print your order information into the order form section STEP 3 - Mail order form and payment to the address below. Make all check or money orders payable to Jumpstart! Please put product 376 on your check or money order. STEP 4 - Include Valid Email Address for Immediate delivery! A email address must be included you will be directed to where to download your software at your email address. For Credit Card Orders Fill out this form and mail in along with credit card number/credit card type/experation date Please print the name on the card clearly. Mail the portion below Jumpstart 1348 Washington Avenue #250 Miami Beach, FL. 33139 Mail-in Order Form Name: ______________________________ > > > > > > Address: _____________________________ > > > > > > City/State/Zip___________________________________________ > > > > > > Email Address:____________________________________ end of form This is a one-time mailing, done by an independent marketing company. We respect your online privacy and apologize if you have received this message in error. We do respect our remove lists! Please do not use the reply to this e-mail, e-mail reply cannot be read! If you would like to be removed from our mailing list just click below and send us an remove request email. Please be aware that any disruption to our remove link prevents those that want to be removed from our database from being removed. Our remove link is barryleden2@dcemail.com. Thank you for your consideration --- From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 12 03:22:31 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3FBCF17AD0; Mon, 12 Jun 2000 03:22:31 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id E033E17ADE; Mon, 12 Jun 2000 03:22:29 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D31EF415DC for ; Mon, 12 Jun 2000 03:22:28 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id DAA28230 for bio-software-list@hgmp.mrc.ac.uk; Mon, 12 Jun 2000 03:22:28 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Brian X-Newsgroups: bionet.software Subject: Shareware/Freeware sequence alignment and assembly programs? Date: Sun, 11 Jun 2000 22:21:38 -0400 Organization: MindSpring Enterprises Lines: 17 Message-ID: Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Server-Date: 12 Jun 2000 02:21:27 GMT User-Agent: Microsoft Outlook Express Macintosh Edition - 5.01 (1630) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Dear bionet software subscribers, I am looking for a shareware/freeware program for the macintosh which will be able to use editseq files generated from the DNAstar programs EditSeq and Seqman for alignment purposes. If there is a program that will do this, will it also save the alignment in NEXUS format? I am hoping to do more work from my home computer and can't afford my personal copy of the DNAStar tools, unless someone has a free copy they can give me. thanks for your help, Brian Teasdale Univ. of New Hampshire P.S. Information on sequence assembly programs would also be appreciated. Please email me responses if possible. teasdale@cisunix.unh.edu From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 12 07:39:46 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C9D5D17AF3; Mon, 12 Jun 2000 07:39:45 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 606FA17A96; Mon, 12 Jun 2000 07:39:44 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id DCDB2415DD for ; Mon, 12 Jun 2000 07:39:43 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA01243 for bio-software-list@hgmp.mrc.ac.uk; Mon, 12 Jun 2000 07:39:43 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: LD334587@cenet.chonbuk.ac.kr X-Newsgroups: bionet.software Subject: 5.5 cents/min Long Distance Calling. All Day. No Fees! Date: 12 Jun 2000 07:39:42 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 31 Message-ID: <1990102080015.GAB07055@cenet.chonbuk.ac.kr> X-Trace: niobium.hgmp.mrc.ac.uk 960791983 1240 193.62.192.80 (12 Jun 2000 06:39:43 GMT) X-Complaints-To: news@net.bio.net X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 2E3C117A96; Mon, 12 Jun 2000 07:39:40 +0100 (BST) X-Received: from relay1.nce.smtp.psi.net (relay1.nce.smtp.psi.net [38.9.152.2]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C3A7A415DD for ; Mon, 12 Jun 2000 07:39:39 +0100 (BST) X-Received: from home.www.psi.ca ([38.8.37.2]) by relay1.nce.smtp.psi.net with esmtp (Exim 3.13 #3) id 131Nso-0003QT-00 for bio-software@net.bio.net; Mon, 12 Jun 2000 02:39:38 -0400 X-Received: from magi.com by home.www.psi.ca (8.8.8+Sun/SMI-SVR4) id CAA22106; Mon, 12 Jun 2000 02:39:28 -0400 (EDT) X-To: bio-software@net.bio.net To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Dear bio-software@net.bio.net, 5.5 cents/min. state to state calling, All Day, No Fees! ...and great international rates for residents INSIDE and OUTSIDE the USA. - Rates apply all day, every day. - No monthly fees or minimums! - 6 second billing increments! - Commercial or residential. - 5.5 cents a minute 800/888 service. - Great international rates! - Direct billing available. .. and International Callback for residents outside the US. We are also looking for agents worldwide to market our services. Great Business Opportunity! For details, contact us at t.jackson@urgentmail.com For service information, please type "5.5" in the subject line. For agent information, please type "agent" in the subject line. Please include your full name when requesting agent information. Thanks. --- From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 12 12:29:11 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id EDD6F17AFB; Mon, 12 Jun 2000 12:29:10 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 99AEB17AF3; Mon, 12 Jun 2000 12:29:09 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id CB08E415CF for ; Mon, 12 Jun 2000 12:29:08 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id MAA04680 for bio-software-list@hgmp.mrc.ac.uk; Mon, 12 Jun 2000 12:29:08 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Andrea Hansen X-Newsgroups: bionet.software Subject: Re: Shareware/Freeware sequence alignment and assembly programs? Date: 12 Jun 2000 13:28:52 +0200 Message-ID: References: X-Trace: fu-berlin.de 960809338 4189448 134.99.202.44 (16 [4974]) X-Newsreader: Gnus v5.5/XEmacs 20.4 - "Emerald" Lines: 17 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Brian writes: > I am looking for a shareware/freeware program for the macintosh which will > be able to use editseq files generated from the DNAstar programs EditSeq and > Seqman for alignment purposes. If there is a program that will do this, > will it also save the alignment in NEXUS format? I am hoping to do more > work from my home computer and can't afford my personal copy of the DNAStar > tools, unless someone has a free copy they can give me. Hi Brian, we have lots of links for mac in our catalog even for your problem: http://www.bioinformatik.de/cgi-bin/browse/Catalog/Software/Mac/Sequence_Analysis/ Andrea -- Institut fuer Botanik III Tel +49 211 81 12339 Heinrich-Heine-Universitaet Fax +49 211 81 13554 Universitaetsstr.1 email : webmaster@bioinformatik.de 40225 Duesseldorf http://www.bioinformatik.de From owner-bio-software@hgmp.mrc.ac.uk Mon Jun 12 14:03:59 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5EF5117AC3; Mon, 12 Jun 2000 14:03:59 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 0884317AAA; Mon, 12 Jun 2000 14:03:57 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 70BCF415E0 for ; Mon, 12 Jun 2000 14:03:57 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA05806 for bio-software-list@hgmp.mrc.ac.uk; Mon, 12 Jun 2000 14:03:56 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Simon Andrews X-Newsgroups: bionet.software Subject: Re: NetPrimer does not work??? Date: Mon, 12 Jun 2000 13:57:53 +0100 Organization: BBSRC Biotechnology and Biological Sciences Research Council Lines: 30 Message-ID: <3944DE51.562C7EAC@bbsrc.ac.uk> References: <3940FA7F.FDD71D19@whoccr.oulu.fi_no_spam> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk There may be a problem using Netprimer under some versions of Netscape. It will work, but is extremely slow. On my machine the Netprimer applet will load under IE4 in about 15 secs, but takes over 3 min using Netscape 4.5. This is from a local copy of the program so network performance shouldn't be an issue. Once it has loaded it works fine under either browser. PN wrote: > > Hi there, > > Does anybody know why NetPrimer (in > http://www.PremierBiosoft.com/netprimer.html) > does not work? > Or does it work in somebody else's computer? > > In my case I think that Applet is running because there is a text in the > > window of Netscape saying "NetPrimerApplet running". The program allows > me > to type in a sequence and even the light in the analyze button turns on > when > I type the 10th letter. But when I click the analyze button nothing > happens. > Did I forget something very simple or is there something strange going > on? I > also tried it in another PC where I even updated Netscape to 4.73 and > program still kept silence. > Any ideas? From owner-bio-software@hgmp.mrc.ac.uk Mon Jun