From owner-software@net.bio.net Sun Aug 01 16:15:00 1999 Path: biosci!fcs280s.ncifcrf.gov!fcrdcnews.NCIFCRF.GOV!washdc3-snf1!crtntx1-snh1.gtei.net!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.direct.ca!dispose.news.demon.net!demon!newsfeed.icl.net!newsfeed.nacamar.de!blackbush.xlink.net!news-kar1.dfn.de!news.embl-heidelberg.de!news.dkfz-heidelberg.de!news.urz.uni-heidelberg.de!not-for-mail From: Andreas Bohne Newsgroups: bionet.software Subject: New Features for RasMol Date: Fri, 30 Jul 1999 10:11:26 +0200 Organization: University of Heidelberg, Germany Message-ID: <37A15E2E.33FA@gmx.de> NNTP-Posting-Host: zsins1.inet.dkfz-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.urz.uni-heidelberg.de 933322346 13436 193.174.61.169 (30 Jul 1999 08:12:26 GMT) X-Complaints-To: usenet@news.urz.uni-heidelberg.de NNTP-Posting-Date: 30 Jul 1999 08:12:26 GMT X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) Lines: 17 hi, I have modiefied R.Sales's RasMol 2.6. This version has 3 new main menus with several submenus. Furthermore this version supports inline scripting and this version is detecting the pixel depth automatically and set this to the working depth. Find this version at http://www.dkfz-heidelberg.de/spec/rasmol2ab2/ At the moment this version is only for Unix but I hope to find time and knowlege to implement the made changes in the Mac and Win version. I have tested this version on Sun, HP, SGI, Linux and SP2. Have fun Andreas From owner-software@net.bio.net Sun Aug 01 16:16:00 1999 Path: biosci!fcs280s.ncifcrf.gov!fcrdcnews.NCIFCRF.GOV!washdc3-snf1!crtntx1-snh1.gtei.net!su-news-hub1.bbnplanet.com!news.gtei.net!news.good.net!newsfeed.enteract.com!news.maxwell.syr.edu!nntp2.deja.com!nnrp1.deja.com!not-for-mail From: zgudmunt@my-deja.com Newsgroups: bionet.software Subject: Sanger´s FPC, problems with Linux Date: Fri, 30 Jul 1999 13:14:53 GMT Organization: Deja.com - Share what you know. Learn what you don't. Lines: 18 Message-ID: <7ns8g5$cov$1@nnrp1.deja.com> NNTP-Posting-Host: 193.4.196.222 X-Article-Creation-Date: Fri Jul 30 13:14:53 1999 GMT X-Http-User-Agent: Mozilla/4.6 [en] (WinNT; I) X-Http-Proxy: 1.0 proxy.decode.is:8080 (Squid/2.1.PATCH2), 1.0 x35.deja.com:80 (Squid/1.1.22) for client 172.18.253.134, 193.4.196.222 X-MyDeja-Info: XMYDJUIDzgudmunt Hi. I hope I´m in the right place. I have been running the fingerprint contig building program FPC from Sanger for a while now. The binary files were for the Sun, but I want to run it also on Linux -> no binaries. The source code does have some Linux definitions, but I can´t get it to compile: make: *** No rule to make target `../fpp/$@', needed by `fpp3.c'. Stop. Has anybody else had this problem? Anybody have a better makefile for me to use? Thanks Gudmundur Sent via Deja.com http://www.deja.com/ Share what you know. Learn what you don't. From owner-software@net.bio.net Sun Aug 01 16:18:00 1999 Path: biosci!fcs280s.ncifcrf.gov!fcrdcnews.NCIFCRF.GOV!washdc3-snf1!crtntx1-snh1.gtei.net!su-news-hub1.bbnplanet.com!news.gtei.net!logbridge.uoregon.edu!newsfeed.icl.net!newsfeed.nacamar.de!bignews.mediaways.net!newsfeed.nettuno.it!server-b.cs.interbusiness.it!not-for-mail From: VV Info Newsgroups: bionet.software Subject: ANN: New soft for Manuals/hypertexts/Internet/CD Date: Fri, 30 Jul 1999 16:52:29 +0200 Organization: Visual Vision Lines: 21 Message-ID: <37A1BC2C.C0E2DB3E@visualvision.com> NNTP-Posting-Host: 194.184.152.58 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [it] (Win95; I) Need to write electronic manuals? Want to create your own autoinstall CD? Want to organize your school works "hypertextually"? In Html or Rtf WinHelp? With WYSIWYG and WYSIWYL? Without complications? If interested, you can try *for free* "iPer", a new fast and productive tool for hypertexts writing, for Win95-98! You can download the demo at: http://visualvision.com/download/d_en3wh.exe "Educational" offers available in our "buy now!" pages. VV Staff (http://visualvision.com/) --------------------------------------------------------------- Visual Vision info@visualvision.com 82, V.le Riviera http://visualvision.com Pietra Ligure - ITALY fax +39-019-625520 --------------------------------------------------------------- From owner-software@net.bio.net Sun Aug 01 16:19:00 1999 Path: biosci!fcs280s.ncifcrf.gov!fcrdcnews.NCIFCRF.GOV!washdc3-snf1!crtntx1-snh1.gtei.net!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.berkeley.edu!newshub.sdsu.edu!franklin.ljcrf.edu!not-for-mail From: greg@franklin.burnham-inst.org (Dr. Greg Quinn) Newsgroups: bionet.software Subject: Linux and bioinformatics questions.... Date: 30 Jul 1999 22:19:23 GMT Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE Lines: 30 Message-ID: <7nt8db$ggv$1@franklin.ljcrf.edu> NNTP-Posting-Host: franklin.ljcrf.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Hi; I will shortly be buying a high end multiprocessor pentium box to perform database searches; I am by no means convinced that Linux is the best operating system for high load activity, and have heard better things about FreeBSD than I have about linux in real-life high-use situations. As far as I can see though, Linux rules in the sense that there are far more supported packages in a molecular biology context. Can somone convince me that Linux must be the way to go for a UNIX PC box? Thanks for any advice. Cheers Greg -- ***************************************** 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 ***************************************** From owner-software@net.bio.net Sun Aug 01 16:21:00 1999 Path: biosci!fcs280s.ncifcrf.gov!fcrdcnews.NCIFCRF.GOV!washdc3-snf1!crtntx1-snh1.gtei.net!su-news-hub1.bbnplanet.com!news.gtei.net!nntp.primenet.com!nntp.gctr.net!newsin.iconnet.net!feed2.nntp.acc.ca!feed.nntp.acc.ca!news.ican.net!not-for-mail From: lidong@globalserve.net (Alex Dong Li) Newsgroups: bionet.software Subject: Re: Batch BLAST Date: 30 Jul 1999 23:53:00 GMT Organization: ICAN.Net Customer Lines: 14 Message-ID: <8E13CADBBlidongglobalservenet@news.globalserve.net> References: NNTP-Posting-Host: dialin210.toronto.globalserve.net User-Agent: Xnews/2.05.21 Why not use webblast? It is designed to do so. The current version runs on unix and windows9x/NT You can get it from http://www.genet.sickkids.on.ca/bioinfo_resources/software.html Alex. >Hi, > Is there a simple way to send off 200 blast searches to NCBI or other >server and have them return the results in HTML or text format? > >Thanks, > Chris From owner-software@net.bio.net Sun Aug 01 16:23:00 1999 Path: biosci!cnn.nas.nasa.gov!newsfeed.berkeley.edu!ctu-gate!news.nctu.edu.tw!news.neto.net!hp1.timenet.net!netnews.hinet.net!news.is.net.tw!news.is.net.tw From: Newsgroups: bionet.software Subject: §Ôµh³Î·R-¸U¤ý¤§¤ý Date: Thu, 29 Jul 1999 21:35:30 PST Organization: The one and only Lines: 7 Message-ID: <07291999213530jaredw@bigfoot.com> NNTP-Posting-Host: h202.s52.s64.t174.dialup.is.net.tw content-length: 134 °â¸U¤ý¤§¤ý¤@®M,©Ò¦³°t¥ó¥]§tÀ²³¹.»¡©ú®Ñ.¦a¹Ïµ¥³£¦b! ÁÙ¥]§t¤@­Ó¤w¸gµ¥¯Å«Ü°ªªºÅ]ªk®v¨¤¦â! NT.600 ¥x¥_¿¤¥«¨Î,¦³·NªÌ¹q:0936-696329 From owner-software@net.bio.net Sun Aug 01 16:24:00 1999 Path: biosci!cnn.nas.nasa.gov!newsfeed.stanford.edu!logbridge.uoregon.edu!dispose.news.demon.net!demon!newsfeed.nacamar.de!newsfeed.nacamar.de!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!not-for-mail From: Tim Cutts Newsgroups: bionet.software Subject: Re: Linux and bioinformatics questions.... Date: 31 Jul 1999 11:27:54 +0100 (BST) Organization: Linux Unlimited Message-ID: References: <7nt8db$ggv$1@franklin.ljcrf.edu> NNTP-Posting-Host: rrw1000.sel.cam.ac.uk Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) Lines: 25 In article <7nt8db$ggv$1@franklin.ljcrf.edu>, Dr. Greg Quinn wrote: >Hi; > >I will shortly be buying a high end multiprocessor pentium box to >perform database searches; I am by no means convinced that Linux is >the best operating system for high load activity, and have heard >better things about FreeBSD than I have about linux in real-life >high-use situations. As far as I can see though, Linux rules >in the sense that there are far more supported packages in a molecular >biology context. > >Can somone convince me that Linux must be the way to go for a UNIX >PC box? Thanks for any advice. Although it is improving all the time, SMP performance on Linux is not wonderful. The latest 2.3 development kernels are supposed to address the issue, but I don't know how stable they are. I can't speak for FreeBSD. I have heard people say that Solaris is still the one to go for for SMP machines; for academics it is not too expensive. Tim. From owner-software@net.bio.net Sun Aug 01 16:24:00 1999 Path: biosci!cnn.nas.nasa.gov!news.msfc.nasa.gov!news.maxwell.syr.edu!intgwpad.nntp.telstra.net!newsfeeds.bigpond.com!not-for-mail From: "kiosk" Subject: Life Game for Differentiation Newsgroups: bionet.software Message-ID: <01bedb53$76cbf880$LocalHost@default> X-Newsreader: Microsoft Internet News 4.70.1155 Lines: 6 Date: Sat, 31 Jul 1999 13:02:54 GMT NNTP-Posting-Host: 139.134.226.107 X-Trace: newsfeeds.bigpond.com 933426174 139.134.226.107 (Sat, 31 Jul 1999 23:02:54 EST) NNTP-Posting-Date: Sat, 31 Jul 1999 23:02:54 EST Organization: Telstra BigPond Internet Services (http://www.bigpond.com) On of the reason why "Life Game" is so interesting may be similar to self-organization in living systems. I tried to simulate the system of cell differentiation with a kind of Life Game. http://www.users.bigpond.com/tiddler/cell.htm From owner-software@net.bio.net Sun Aug 01 17:18:00 1999 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newspump.monmouth.com!newspeer.monmouth.com!hermes.visi.com!news-out.visi.com!cam-news-hub1.bbnplanet.com!news.gtei.net!newscon02!prodigy.com!not-for-mail From: Newsgroups: bionet.software Subject: AutoExec2000.com Date: 31 Jul 1999 07:39:56 GMT Organization: Prodigy Internet http://www.prodigy.com Lines: 3 Message-ID: <7nu98c$3vf0$9606@newssvr04-int.news.prodigy.com> NNTP-Posting-Host: miamb109-23.splitrock.net X-Trace: newssvr04-int.news.prodigy.com 933406796 3767148 209.156.29.92 (31 Jul 1999 07:39:56 GMT) X-Complaints-To: abuse@prodigy.net NNTP-Posting-Date: 31 Jul 1999 07:39:56 GMT Just ran across this great web site, I thought you would be very interested in! http://www.AutoExec2000.com From owner-software@net.bio.net Sun Aug 01 17:20:00 1999 Path: biosci!fcs280s.ncifcrf.gov!fcrdcnews.NCIFCRF.GOV!washdc3-snf1!crtntx1-snh1.gtei.net!cam-news-feed2.bbnplanet.com!news.gtei.net!homer.alpha.net!solaris.cc.vt.edu!news.vt.edu!newsfeed.berkeley.edu!cyclone.bc.net!cyclone.mbnet.mb.ca!typhoon.mbnet.mb.ca.POSTED!not-for-mail From: "*" Newsgroups: alt.games.quake3,alt.games.unreal.ed,alt.geo-software,alt.sex.children,alt.startrek.steg,alt.video.digital-tv,alt.video.dvd.tech,alt.video.games,amiga.software,at.tuwien.software,bionet.software,bionet.software.pc,clari.tw.computers.pc.hardwar Subject: WANNA MAKE $200 OR MORE A MONTH FOR DOING BASICALLY NOTHING Lines: 18 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Message-ID: Date: Sun, 01 Aug 1999 04:29:07 GMT NNTP-Posting-Host: 216.81.25.164 X-Trace: typhoon.mbnet.mb.ca 933481747 216.81.25.164 (Sat, 31 Jul 1999 23:29:07 CDT) NNTP-Posting-Date: Sat, 31 Jul 1999 23:29:07 CDT Organization: MBnet Networking Inc. 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(19612) Date: 1 Aug 1999 23:14:51 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 34 Message-ID: <59842.22473@mail.mailworksnow.net> NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 933545692 20414 193.62.192.80 (1 Aug 1999 22:14:52 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 1 Aug 1999 22:14:52 GMT X-Received: from mserv1.dl.ac.uk (root@mserv1.dl.ac.uk [148.79.160.65]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id XAA02255; Sun, 1 Aug 1999 23:14:48 +0100 (BST) X-Received: from mail.mailworksnow.net (1Cust162.tnt3.sfo3.da.uu.net [153.37.9.162]) by mserv1.dl.ac.uk with SMTP id XAA10431 (8.8.8/5.4[ref postmaster@dl.ac.uk] for dl.ac.uk from adv2000@nfmail.com); Sun, 1 Aug 1999 23:14:44 +0100 (BST) X-Precedence: first-class ACCEPT CREDIT CARDS OVER THE INTERNET AND INCREASE YOUR SALES DRAMATICALLY! *Everyone is accepted and we'll EVEN WAIVE THE SETUP FEES!! *Multilevel Marketing *Mail Order/ Phone Sales *Home Based Business *INTERNET BASED BUSINESS *New Business* Small Business Everyone Is Welcome! Regardless of your credit rating, WE GUARANTEE YOUR APPROVAL!! CALL NOW 1(800) 263-4721 ************************************************************************************* This message is sent in compliance of the new email bill section 301. Per Section 301, Paragraph (a)(2)(C) of S. 1618, further transmissions to you by the sender of this email may be stopped at no cost to you. TO REMOVE CLICK ON mailto:delete10@nfmail.com?subject=remove ************************************************************************************* ********************* 68109 --- From owner-software@net.bio.net Sun Aug 01 23:26:00 1999 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!hermes.visi.com!news-out.visi.com!nntp.giganews.com!nntp1.hal-pc.org!news.hal-pc.org!not-for-mail From: "F. Dail Singleton, Jr." Newsgroups: bionet.software Subject: EDTECH Shareware Again Date: Sun, 01 Aug 1999 19:18:11 -0500 Organization: Houston Area League of PC Users, Inc. Lines: 19 Message-ID: <37A4E3C3.28C7@hal-pc.org> Reply-To: fdails@DAofTX.com NNTP-Posting-Host: 206.180.128.7.dial-ip.hal-pc.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.04 (Win95; I) About 2 weeks ago EDTECH (EDitor for TECHnical graphics) V3.0 was newly made available on the web, but since then more testing revealed so many problems that we have produced V3.01 with many internal changes. Those of you who already downloaded it should do so again, and I apologize for the repeat. Now memory use is actually less so that it can run slowly on an 8Mb machine. See its description and download the trial version (same features as regular version) at http://www.DAofTX.com EDTECH 3.01 for Win95/98/NT lets you produce scientific-style XY-plots and other high-resolution, highly detailed black-and-white line graphics suitable for publication in technical reports and journals. Dail Singleton, PhD Digital Analytics of Texas fdails@DAofTX.com From owner-software@net.bio.net Mon Aug 02 03:31:00 1999 Path: biosci!ACCEFYN.ORG.CO!acad From: acad@ACCEFYN.ORG.CO (Alex Garcia) Newsgroups: bionet.software Subject: srs Date: 1 Aug 1999 21:31:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <37A515F0.883D694A@accefyn.org.co> NNTP-Posting-Host: net.bio.net I would like to know if this is possible: having a LAN running under linux or win (with a WEB server for local consult) would I be able to install the SRS and some databases and allow my users to check this local implementation of the SRS¿ cif this is possible where can I find info abot local implementations of SRS From owner-software@net.bio.net Mon Aug 02 05:55:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newsfeed.berkeley.edu!newsgate.cuhk.edu.hk!hkusud.hku.hk!hkunae.hku.hk!hkusub.hku.hk!not-for-mail From: Xia Xuhua Newsgroups: bionet.software Subject: New version of DAMBE Date: 2 Aug 1999 01:56:48 GMT Organization: The University of Hong Kong Lines: 92 Message-ID: <7o2tt0$mnc1@hkunae.hku.hk> NNTP-Posting-Host: hkusub.hku.hk Summary: Phylogenetics, Molecular evolution, comparative sequence analysis, bioinformatics Keywords: Phylogenetics, Molecular evolution, comparative sequence analysis, bioinformatics X-Newsreader: TIN [UNIX 1.3 release 961025] Dear All, I have just uploaded a new version of DAMBE to my URL site: http://web.hku.hk/~xxia/software/software.htm One particular enhancement that I wish to highlight is the statistical tests of alternative phylogenetic hypotheses by using distance (Fitch-Margoliash method), maximum parsimony, and maximum likelihood methods. In short, you provide alternative phylogenetic hypotheses represented by different tree topologies in a file in PHYLIP format, and DAMBE will evaluate relative statistical support for each of the topologies relative to the best. It takes just a few mouse clicks to perform these tests. Here is a brief rational of the tests: 1. For Fitch-Margoliash method: the test is based on the fit to the distance matrix. DAMBE calculates the distance matrix based on the distance you specify, evaluates tree branch lengths for each of the UNROOTED topologies in the user tree file (or all possible topologies generated in DAMBE), and obtains the pairwise distances based on the estimated tree branch lengths. The differences between these pair-wise distances and those in the original distance matrix are them calculated, so are the variance of the differences. If the differences are all zero (perfect fit), then the variance is zero. If the fit is poor, then you have a large variance. If you have 10 user trees, then you have 10 variances, and the best tree is the one with the smallest variance. A Bartlett's test of homogeneity of variance is then carried out as an overall test. If the test is not significant, then you may stop there and conclude that the best tree is not significantly better than others. If the test is significant, then you can use multiple comparisons to test whether each alternative topology is worse than the best tree. To adjust for the experimentwise error rate associated with multiple comparisons, a test analogous to Newman-Keuls test (which is based on the same statistic as Tukey's HSD test) is applied with q calculated as q = (ln(VarA)-ln(VarB))/SE The main weakness of the test is that the distances in the distance matrix are not statistically independent of each other. The main advantage of the test is that it should be very powerful in rejecting poor topologies. The qualify of the test, of course, depends entirely on how appropriate the genetic distances are. 2. For the maximum parsimony method, a ROOTED tree is required to represent alternative topologies. This limitation arises from DAMBE's inheritance of the code from DNAPARS in Joe's PHYLIP. DNAPARS has already provided a significance test if you provide user trees. In short, it computes the number of steps (changes in character states) for each topology, the difference in the number of steps between the best and each alternative topology, and the associated (large-sample) variance of the differences. The z-score is computed and declared as significant if it is larger than 1.96. The main problem with this test is that the result can be interpreted probabilistically only when you have just two topologies and is not appropriate with multiple comparisons. DAMBE uses Newman-Keuls test which is valid for multiple comparisons. 3. For the maximum likelihod method, the Kishino-Hasegawa test (RELL) is implemented as in PAML whose code I have used, again with the adjustment for multiple comparisons. The Kishino-Hasegawa test, as is practiced in literature, is analogous to the test in DNAPARS, except that the test is based on likelihood instead on the number of steps. In short, you calculate the maximum likelihood for each topology, the difference in likelihood between the best tree and each alternative topologies, and the variance of the differences estimated by resampling. The z-score is then calculated and declared as significant if it is larger than 1.96. Again, such interpretation is heuristic and is not appropriate probabilistically if there are more than two topologies being compared. DAMBE uses Newman-Keuls test which is valid for multiple comparisons. To perform one of these tests in DAMBE, you open a sequence file with aligned sequences. Click PHYLOGENETICS menu and then one of the three submenus: (DISTANCE, MAXIMUM PARSIMONY or MAXIMUM LIKELIHOOD). When the dialog box appears, click the USERTREE option. A standard file OPEN|SAVE dialog box appears for you to choose the file containing user trees in PHYLIP format (alternatively you may click the option for all possible trees if the number of OTUs are small, e.g., 5 or 6). Click whatever other options according to your intuition, and then the DONE button. DAMBE will carry out the test (It may take a long time with the maximum likelihood method). Best. Xuhua ================================================================== Dr. Xuhua Xia | Tel: (852) 2857 8239 (lab) Dept. Ecol. & Biod. | Tel: (852) 2975 5629 (office) Rm 603, T.T. Tsui Building | Fax: (852) 2517 6082 The University of Hong Kong | Email: xxia@hkusua.hku.hk Pukfulam Road | WWW: http://web.hku.hk/~xxia Hong Kong | ================================================================== From owner-software@net.bio.net Mon Aug 02 09:33:00 1999 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!dispose.news.demon.net!demon!colt.net!newsfeed.icl.net!bignews.mediaways.net!news3-muc.ecrc.net!newsfeed2.ecrc.net!news.ecrc.de!not-for-mail From: Thomas Busl Newsgroups: bionet.software Subject: Re: Linux and bioinformatics questions.... Date: Mon, 02 Aug 1999 12:26:10 +0200 Organization: ECRC Message-ID: <37A57241.BAF5EE2B@micromet.de> References: <7nt8db$ggv$1@franklin.ljcrf.edu> NNTP-Posting-Host: delta.m.infra.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (WinNT; I) Lines: 37 Dear Tim, I work with solaris on sparc and I think you are right about SMP workstations. You can see that sun has alot of expiriences in that field. I think you get solaris2.6 free for intel plattforms. so long thomas Tim Cutts wrote: > In article <7nt8db$ggv$1@franklin.ljcrf.edu>, > Dr. Greg Quinn wrote: > >Hi; > > > >I will shortly be buying a high end multiprocessor pentium box to > >perform database searches; I am by no means convinced that Linux is > >the best operating system for high load activity, and have heard > >better things about FreeBSD than I have about linux in real-life > >high-use situations. As far as I can see though, Linux rules > >in the sense that there are far more supported packages in a molecular > >biology context. > > > >Can somone convince me that Linux must be the way to go for a UNIX > >PC box? Thanks for any advice. > > Although it is improving all the time, SMP performance on Linux is not > wonderful. The latest 2.3 development kernels are supposed to address > the issue, but I don't know how stable they are. > > I can't speak for FreeBSD. > > I have heard people say that Solaris is still the one to go for for > SMP machines; for academics it is not too expensive. > > Tim. From owner-software@net.bio.net Mon Aug 02 10:23:00 1999 Path: biosci!hsr.it!niojoulo58 From: niojoulo58@hsr.it (jo8r543y) Newsgroups: bionet.software Subject: Make 10K A Month, Famous Private-Eye Tells All Date: 2 Aug 1999 04:22:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 101 Sender: daemon@net.bio.net Distribution: world Message-ID: <19990802421SAA6040@gth6stop764r.ciatej.net.mx> NNTP-Posting-Host: net.bio.net Oprah, Nightline, Maria Shriver, 48 Hours, 20/20 and more have all interviewed this famous Private Investigator. Now, you too can make substantial income using Schweitzers highly sought- after SECRETS. Thank you for your interest in our training Course! Judgment Acquisition & Recovery, Inc. offers an extensive training course in "How to Collect Judicial Judgments". If you are like many people, you are not even sure what a Judicial Judgment is and why processing Judicial Judgments can earn you very substantial income. 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Please call us at 1-888-309-5852 (Toll Free) and speak with Al Schweitzer directly (between the hours of 9:00am - 5:00pm, Mountain Time) Thank you for your time and interest. rem -ko987@excite.com From owner-software@net.bio.net Mon Aug 02 10:54:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!oleane!jussieu.fr!univ-angers.fr!ciril.fr!news.u-strasbg.fr!not-for-mail From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: Linux and bioinformatics questions.... Date: 2 Aug 1999 12:50:51 GMT Organization: CRC - Universite Louis Pasteur Strasbourg France Lines: 16 Message-ID: <7o447b$h5a$1@news.u-strasbg.fr> References: <7nt8db$ggv$1@franklin.ljcrf.edu> <37A57241.BAF5EE2B@micromet.de> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.u-strasbg.fr 933598251 17578 130.79.79.13 (2 Aug 1999 12:50:51 GMT) X-Complaints-To: usenet@u-strasbg.fr NNTP-Posting-Date: 2 Aug 1999 12:50:51 GMT X-Newsreader: knews 1.0b.0 Mail-Copies-To: never In article <37A57241.BAF5EE2B@micromet.de>, Thomas Busl writes: > Dear Tim, > I work with solaris on sparc and I think you are right about SMP > workstations. You can see that sun has alot of expiriences in that field. I > think you get solaris2.6 free for intel plattforms. > so long Actually, with big databases, the problem is not Linux vs Solaris (Because, Linux runs well on a Sparc SMP), but 32 vs 64 bits processors. And in this field, it could be good to test a Alpha. The "old" 21164PC runs at 533MHz and can handle 128bits bus at 100MHz. For a low price 64bits calculator, you could consider making a beowulf linux clusteer of such machines. François. From owner-software@net.bio.net Mon Aug 02 13:03:00 1999 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!jkb From: jkb@mrc-lmb.cam.ac.uk (James Bonfield) Newsgroups: bionet.software,bionet.software.staden Subject: Staden Package sequencing course Date: 2 Aug 1999 13:56:30 GMT Organization: MRC Laboratory of Molecular Biology, Cambridge UK Lines: 29 Distribution: world Message-ID: <7o482e$i3i$1@pegasus.csx.cam.ac.uk> NNTP-Posting-Host: alf2.mrc-lmb.cam.ac.uk Keywords: Staden, Gap4, course Xref: biosci bionet.software:23905 bionet.software.staden:1017 In October 21st to 23rd inclusively, there is a course entitled "Sequence Project Management Using the Staden Package". Full details may be found on: http://www.ib3.gmu.edu/educate/oct.stadencourse/stadencourse.html A summary follows: The course is designed to provide an introduction to the use of the latest version of programs produced by Rodger Staden's group for the management of large-scale DNA sequencing projects. The course is very practical. Participants will be guided through exercises during which they will process a substantial set of sequence data obtained from an ABI automatated DNA sequencers. In the course of the three days we will cover setting up of a new sequencing project, pre-processing data generated by automatic sequencers, creating sequencing project databases, automatic assembly of batches of reads into contigs, checking and editing contigs, and use of phred-style confidence values. Checking will include examination of the traces for conflicting readings, searches for repeated sequences and analysis of the relative positions of readings derived from the same template. -- James Bonfield (jkb@mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556 Medical Research Council - Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/ From owner-software@net.bio.net Mon Aug 02 15:49:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!dispose.news.demon.net!demon!colt.net!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!is.bbsrc.ac.uk!news From: Aedin Culhane Newsgroups: bionet.software Subject: Plasmid drawing packages Date: Mon, 02 Aug 1999 17:34:23 +0100 Organization: BITS BBSRC Message-ID: <37A5C88F.F7D3A3C5@bbsrc.ac.uk> NNTP-Posting-Host: pc0635.cc.bbsrc.ac.uk 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 Lines: 8 I have seen commercial programs like Clonemap which seem very nice, but really need a freeware/shareware plasmid drawing package. I have tried pDraw32 and Plasmid Processor Pro, but neither seem to produce colour graphics (in my hands). I am grateful for any help Aedin From owner-software@net.bio.net Tue Aug 03 06:04:00 1999 Path: biosci!HJ.SE!gefuume63 From: gefuume63@HJ.SE (Fine Tuning) Newsgroups: bionet.software Subject: Cable TV .......New, Improved, Enhanced. Date: 3 Aug 1999 00:04:03 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 178 Sender: daemon@net.bio.net Distribution: world Message-ID: <199908023601CAA41217@funNeasy.co.ru> NNTP-Posting-Host: net.bio.net This is really COOL! ENHANCE Your Cable TV! EASY to assemble plans for only $7.00 ! GET THE MOST out of your cable TV by using this SIMPLE "Fine Tuning" device! YOU WILL HAVE GREAT RESULTS! YOU will be enjoying enhanced cable viewing in just a few days! This Cable TV FINE TUNING DEVICE will make your viewing experince MUCH MORE ENJOYABLE! There is one problem though. It may accidentally receive stations that NORMALLY are offered by your cable provider for an additional fee. This would include: BOX OFFICE HIT MOVIES! 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You will need these easy to obtain parts : 270-235 mini box 271-1325 2.2k ohm resistor 278-212 chasis connectors RG59 coaxial cable #12 copper wire Variable capacitor They may have to special order the variable capacitor, But WHY WAIT for a special order? WE have them! WE have secured a supply of the capacitors directly from the manufacturer and We WILL include one with your plans for an ADDITIONAL $10.00 only! All you need now is the EASY TO ASSEMBLE plans to show you how to assemble this educational device in 30 MINUTES! It is LEGAL, providing of course you use these plans for EDUCATIONAL PURPOSES only. See first hand and LEARN how this SIMPLE circuitry works! If you intend to use these plans for any other purpose DO NOT ORDER them. IT'S FUN TO BUILD! We're sure you'll enjoy this project! This is a unique opportunity for hobbiest of ANY skill level to learn simple circuitry! Learn how easy "Fine Tuning" is! $ 7.00 for plans only $10.00 for variable capacitor only $17.00 for The easy to assemble plans and one variable capacitor! Please send check or money order payable to: FINE TUNING PMB #287 99 Park Ave. New York, N.Y. 10016 WE pay postage and handling! Please allow 10 days for delivery. Thank You /\ \/ /\ From owner-software@net.bio.net Tue Aug 03 07:13:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!isdnet!pasteur.fr!jussieu.fr!univ-angers.fr!not-for-mail From: "Yves TOURMEN" Newsgroups: bionet.software Subject: RasMol Windows 98 Date: Tue, 3 Aug 1999 10:08:42 +0200 Organization: University of Angers, France. Lines: 8 Message-ID: <7o6809$2u50$1@news.univ-angers.fr> NNTP-Posting-Host: fw01.chu-angers.fr X-Trace: news.univ-angers.fr 933667657 96416 193.51.213.250 (3 Aug 1999 08:07:37 GMT) X-Complaints-To: newsmaster@univ-angers.fr NNTP-Posting-Date: 3 Aug 1999 08:07:37 GMT X-Newsreader: Microsoft Outlook Express 4.72.3612.1700 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 Where can I find the latest version of Rasmol under W98 ? Thanks Yves Tourmen yvtourmen@chu-angers.fr From owner-software@net.bio.net Tue Aug 03 18:16:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Paraic Kenny Newsgroups: bionet.software Subject: unBLASTable sequence? Date: Tue, 03 Aug 1999 19:16:40 +0000 Organization: Institute of Cancer Research Lines: 51 Sender: pkenny@cbp241.icr.ac.uk Message-ID: <37A74013.61AEDC92@icr.ac.uk> Reply-To: paraic@icr.ac.uk NNTP-Posting-Host: cbp241.icr.ac.uk Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------895197374814AFBD0CF57189" X-Trace: niobium.hgmp.mrc.ac.uk 933707379 1053 193.63.217.241 (3 Aug 1999 19:09:39 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 3 Aug 1999 19:09:39 GMT X-Mailer: Mozilla 4.61 (Macintosh; I; PPC) X-Accept-Language: en This is a multi-part message in MIME format. --------------895197374814AFBD0CF57189 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Hi all, I was trying to BLAST a protein sequence today at the NCBI blast server and in the results, part of my query sequence came up as a row of XXXXXXXXs even though it is directly identical to a sequence in the databases. The "unBLASTable" part of the sequence is arqpppaprsappsppfppppafp I have also checked it using a different BLAST server with the same result. Can anybody explain why the server can't / won't accept this sequence? Thanks Paraic Kenny --------------895197374814AFBD0CF57189 Content-Type: text/x-vcard; charset=us-ascii; name="paraic.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Paraic Kenny Content-Disposition: attachment; filename="paraic.vcf" begin:vcard n:Kenny;Paraic tel;fax:+44 (0) 171 352 3299 tel;work:+44 (0) 171 352 8133 x5261 x-mozilla-html:FALSE url:http://www.icr.ac.uk org:Gene Function and Regulation;Institute of Cancer Research adr:;;237 Fulham Road;London;;SW3 6JB;UK version:2.1 email;internet:paraic@icr.ac.uk title:PhD student x-mozilla-cpt:;1 fn:Paraic Kenny end:vcard --------------895197374814AFBD0CF57189-- From owner-software@net.bio.net Tue Aug 03 18:49:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!dispose.news.demon.net!demon!newsfeed.icl.net!newsfeed.tli.de!newsfeed01.btx.dtag.de!newsfeed.pop.de!uucp.muenster.de!news.citykom.de!not-for-mail From: Paul Elsinghorst Newsgroups: bionet.software Subject: Re: RasMol Windows 98 Date: Tue, 03 Aug 1999 21:44:25 +0200 Organization: Citykom Muenster GmbH Message-ID: <37A74699.A1AFD4DB@muenster.de> References: <7o6809$2u50$1@news.univ-angers.fr> NNTP-Posting-Host: mueamc-wan132.citykom.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Server-Date: 3 Aug 1999 19:43:07 GMT X-Mailer: Mozilla 4.51 [de]C-CCK-MCD QXW03200 (Win95; I) X-Accept-Language: de,en Lines: 21 Hey, you probably wanna check out the following adress: http://www.dkfz-heidelberg.de/spec/rasmol2ab2/ This version runs on all UNIX-like builds. C YA, Paul Yves TOURMEN schrieb: > Where can I find the latest version of Rasmol under W98 ? > > Thanks > > Yves Tourmen > yvtourmen@chu-angers.fr From owner-software@net.bio.net Tue Aug 03 23:30:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!nntp.kreonet.re.kr!usenet.seri.re.kr!bioneer.kaist.ac.kr!dykim From: dykim@bioneer.kaist.ac.kr (Dooyeon Kim) Newsgroups: bionet.software Subject: Web sites for PCR primer design Date: 4 Aug 1999 00:25:16 GMT Organization: Dept. of Biological Sciences, KAIST Lines: 17 Message-ID: <7o819c$o8r$1@green.kreonet.re.kr> NNTP-Posting-Host: bioneer.kaist.ac.kr X-Newsreader: TIN [version 1.2 PL2] Hi, Does anyone know the web site for PCR primer design? I have been using http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi primer 3 service but sometimes I found that the resulting primer was dimeric configuration. Please tell me the annother site for PCR primer design. -- ___________________________________________________________________________ Ajou medical school Dooyeon Kim ...................... Pharmacology Lab. dykim@bioneer.kaist.ac.kr ___________________________________________________________________________ From owner-software@net.bio.net Wed Aug 04 02:22:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news-out.uswest.net!news.uswest.net!not-for-mail Message-ID: <37A7AFCD.AA5B2911@bioreason.com> From: Andrew Dalke Organization: Bioreason, Inc. X-Mailer: Mozilla 4.05C-SGI [en] (X11; U; IRIX64 6.5 IP30) MIME-Version: 1.0 Newsgroups: bionet.software Subject: Re: unBLASTable sequence? References: <37A74013.61AEDC92@icr.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 14 Date: Tue, 03 Aug 1999 21:13:17 -0600 NNTP-Posting-Host: 207.108.245.3 X-Trace: news.uswest.net 933736559 207.108.245.3 (Tue, 03 Aug 1999 22:15:59 CDT) NNTP-Posting-Date: Tue, 03 Aug 1999 22:15:59 CDT Paraic Kenny said: > I was trying to BLAST a protein sequence today at the NCBI blast > server and in the results, part of my query sequence came up as a > row of XXXXXXXXs even though it is directly identical to a sequence > in the databases. See http://www.ncbi.nlm.nih.gov/BLAST/filtered.html . Redo your search and untoggle the filtering checkbox. By default the NCBI BLAST searchs mask out regions of low complexity. I imagine other sites do so as well. Andrew Dalke dalke@bioreason.com From owner-software@net.bio.net Wed Aug 04 03:02:00 1999 Path: biosci!ECNET.EC!jumoline From: jumoline@ECNET.EC ("Julio Molineros") Newsgroups: bionet.software Subject: unsubscribe Date: 3 Aug 1999 21:02:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <199908040349.WAA90494@ecnet.ec> Reply-To: jumoline@ECNET.ec NNTP-Posting-Host: net.bio.net unsubscribe Julio Molineros Internet: jumoline@pi.pro.ec From owner-software@net.bio.net Wed Aug 04 06:16:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!dispose.news.demon.net!demon!newsfeed.tli.de!easynet-fr!ciril.fr!news.u-strasbg.fr!not-for-mail From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: unBLASTable sequence? Date: 4 Aug 1999 08:12:53 GMT Organization: CRC - Universite Louis Pasteur Strasbourg France Message-ID: <7o8sm5$do2$1@news.u-strasbg.fr> References: <37A74013.61AEDC92@icr.ac.uk> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.u-strasbg.fr 933754373 14082 130.79.79.13 (4 Aug 1999 08:12:53 GMT) X-Complaints-To: usenet@u-strasbg.fr NNTP-Posting-Date: 4 Aug 1999 08:12:53 GMT X-Newsreader: knews 1.0b.0 Mail-Copies-To: never Lines: 20 In article <37A74013.61AEDC92@icr.ac.uk>, Paraic Kenny writes: > The "unBLASTable" part of the sequence is > > arqpppaprsappsppfppppafp > > > I have also checked it using a different BLAST server with the same > result. > > Can anybody explain why the server can't / won't accept this sequence? It is filtered due to its low complexity. Removing the filters as suggested by Andrew will "flood" your output with lot of poly-prolines sequences, with no biological means nor informations. You could try, once. François. From owner-software@net.bio.net Wed Aug 04 06:25:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!isdnet!oleane!jussieu.fr!univ-angers.fr!not-for-mail From: "Yves TOURMEN" Newsgroups: bionet.software Subject: Re: Web sites for PCR primer design Date: Wed, 4 Aug 1999 09:20:06 +0200 Organization: University of Angers, France. Lines: 38 Message-ID: <7o8ph8$12o7$1@news.univ-angers.fr> References: <7o819c$o8r$1@green.kreonet.re.kr> NNTP-Posting-Host: fw01.chu-angers.fr X-Trace: news.univ-angers.fr 933751144 35591 193.51.213.250 (4 Aug 1999 07:19:04 GMT) X-Complaints-To: newsmaster@univ-angers.fr NNTP-Posting-Date: 4 Aug 1999 07:19:04 GMT X-Newsreader: Microsoft Outlook Express 4.72.3612.1700 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 Hi You can try the french site : http://www.citi2.fr/bio2/Oligo2lib.html I think it doesn't matter if you don't speak french, because the results are easy to understand. Bye Yves Tourmen CHU Angers France Tel : 02 41 35 33 14 fax : 02 41 35 40 17 e-mail : yvtourmen@chu-angers.fr Dooyeon Kim a écrit dans le message <7o819c$o8r$1@green.kreonet.re.kr>... >Hi, > >Does anyone know the web site for PCR primer design? > >I have been using http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi > >primer 3 service but sometimes I found that the resulting primer was dimeric > >configuration. Please tell me the annother site for PCR primer design. > >-- >___________________________________________________________________________ > > Ajou medical school Dooyeon Kim ...................... > Pharmacology Lab. dykim@bioneer.kaist.ac.kr >___________________________________________________________________________ > From owner-software@net.bio.net Wed Aug 04 06:30:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newsfeed.icl.net!newsfeed1.news.nl.uu.net!sun4nl!tank.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!scarp.sanger.ac.uk!birney From: Ewan Birney Newsgroups: bionet.software Subject: wise2.1.20c released Date: Wed, 4 Aug 1999 08:22:57 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 17 Message-ID: NNTP-Posting-Host: scarp.sanger.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 933751379 17778 193.60.84.227 (4 Aug 1999 07:22:59 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 4 Aug 1999 07:22:59 GMT A stable release of the Wise2 package, 2.1.20c has been released. More information can be found from http://www.sanger.ac.uk/Software/Wise2/ This includes web forms to try out the algorithms Wise2 includes the genewise algorithm, which can compare genomic DNA directly to proteins or protein hidden Markov models, predicted introns and frameshifts on the fly. Ewan Birney http://www.sanger.ac.uk/Users/birney/ From owner-software@net.bio.net Wed Aug 04 06:54:00 1999 Path: biosci!COMPUSERVE.COM!7u8345104 From: 7u8345104@COMPUSERVE.COM Newsgroups: bionet.software Subject: Get Your BA, MA,MBA,PHD.. Date: 4 Aug 1999 00:54:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <199908040659.IAA04981@dns.arcanset.fr> NNTP-Posting-Host: net.bio.net UNIVERSITY DIPLOMAS Obtain a prosperous future, money earning power, and the admiration of all. Diplomas from prestigious non-accredited universities based on your present knowledge and life experience. 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NOT MLM. *FREE INFO 24 HOUR MESSAGE CALL 1-416-410-7530 rem - mike_watters998.yahoo.com tA From owner-software@net.bio.net Wed Aug 04 08:39:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!dispose.news.demon.net!demon!btnet-peer!btnet!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Paraic Kenny Newsgroups: bionet.software Subject: Re: Web sites for PCR primer design Date: Wed, 04 Aug 1999 09:39:10 +0000 Organization: Institute of Cancer Research Sender: pkenny@cbp241.icr.ac.uk Message-ID: <37A80A3C.F62628FE@icr.ac.uk> References: <7o819c$o8r$1@green.kreonet.re.kr> Reply-To: paraic@icr.ac.uk NNTP-Posting-Host: cbp241.icr.ac.uk Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------99278DA0D2F337CC2BFFD25A" X-Trace: niobium.hgmp.mrc.ac.uk 933759132 19460 193.63.217.241 (4 Aug 1999 09:32:12 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 4 Aug 1999 09:32:12 GMT X-Mailer: Mozilla 4.61 (Macintosh; I; PPC) X-Accept-Language: en Lines: 41 This is a multi-part message in MIME format. --------------99278DA0D2F337CC2BFFD25A Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit You can try: http://bibiserv.techfak.uni-bielefeld.de/cgi-bin/gf_submit?mode=STARTUP&sample=dna All the primers I've selected using this site have worked. Paraic Kenny --------------99278DA0D2F337CC2BFFD25A Content-Type: text/x-vcard; charset=us-ascii; name="paraic.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Paraic Kenny Content-Disposition: attachment; filename="paraic.vcf" begin:vcard n:Kenny;Paraic tel;fax:+44 (0) 171 352 3299 tel;work:+44 (0) 171 352 8133 x5261 x-mozilla-html:FALSE url:http://www.icr.ac.uk org:Gene Function and Regulation;Institute of Cancer Research adr:;;237 Fulham Road;London;;SW3 6JB;UK version:2.1 email;internet:paraic@icr.ac.uk title:PhD student x-mozilla-cpt:;1 fn:Paraic Kenny end:vcard --------------99278DA0D2F337CC2BFFD25A-- From owner-software@net.bio.net Wed Aug 04 13:40:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!oleane!jussieu.fr!univ-angers.fr!not-for-mail From: "Yves TOURMEN" Newsgroups: bionet.software Subject: Re: Web sites for PCR primer design Date: Wed, 4 Aug 1999 16:35:14 +0200 Organization: University of Angers, France. Lines: 34 Message-ID: <7o9j12$1eqn$1@news.univ-angers.fr> References: <7o819c$o8r$1@green.kreonet.re.kr> NNTP-Posting-Host: fw01.chu-angers.fr X-Trace: news.univ-angers.fr 933777250 47959 193.51.213.250 (4 Aug 1999 14:34:09 GMT) X-Complaints-To: newsmaster@univ-angers.fr NNTP-Posting-Date: 4 Aug 1999 14:34:09 GMT X-Newsreader: Microsoft Outlook Express 4.72.3612.1700 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 Hi You can try the sites described on the Web page : http://www-biol.univ-mrs.fr/biologie/logligne.html (search PCR) Bye Yves Tourmen Laboratoire de Biochimie Biologie Moleculaire CHU Angers Tel : 02 41 35 33 14 Fax : 02 41 35 40 17 Email : yvtourmen@chu-angers.fr Dooyeon Kim a écrit dans le message <7o819c$o8r$1@green.kreonet.re.kr>... >Hi, > >Does anyone know the web site for PCR primer design? > >I have been using http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi > >primer 3 service but sometimes I found that the resulting primer was dimeric > >configuration. Please tell me the annother site for PCR primer design. > >-- >___________________________________________________________________________ > > Ajou medical school Dooyeon Kim ...................... > Pharmacology Lab. dykim@bioneer.kaist.ac.kr >___________________________________________________________________________ > From owner-software@net.bio.net Wed Aug 04 15:15:00 1999 Message-ID: <37A86595.150E0918@Genetik.Uni-Bielefeld.DE> Date: Wed, 04 Aug 1999 18:08:53 +0200 From: Frank Vorhoelter Organization: Biologie VI (Genetik); Universitaet Bielefeld X-Mailer: Mozilla 4.51 [en] (X11; I; SunOS 5.6 sun4u) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software Subject: Free sequence conversion software? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: hawaii.genetik.uni-bielefeld.de X-Trace: 4 Aug 1999 18:08:54 +0200, hawaii.genetik.uni-bielefeld.de Lines: 13 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.nacamar.de!newsfeed.nacamar.de!blackbush.xlink.net!news-kar1.dfn.de!news-han1.dfn.de!news.uni-bielefeld.de!hawaii.genetik.uni-bielefeld.de I hope this question is not too boring, but I'm looking for tool to convert data in EMBL feature table (FT) format to GenBank format. Is there anything free I could ask my UNIX administrator to install? I would appreciate any helpful hints. Frank -- Frank-Joerg Vorhoelter Biologie VI (Genetik) Tel. ++49-(0)521-1062036 Universitaet Bielefeld Fax ++49-(0)521-1065626 Universitaetsstr. 25 D-33615 Bielefeld e-mail frank@genetik.uni-bielefeld.de Germany From owner-software@net.bio.net Wed Aug 04 15:21:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news2.best.com!news3.best.com!nntp1.ba.best.com!not-for-mail From: Alan Williams Subject: [Announce] www.MolBio.org -- New Biology Portal Newsgroups: bionet.general,bionet.software,bionet.info-theory,bionet.molec-model,bionet.cellbiol,bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.plants,bionet.plants.education Followup-To: bionet.general Summary: User-Agent: tin/pre-1.4-980818 ("Laura") (UNIX) (FreeBSD/2.2.8-STABLE (i386)) Date: 04 Aug 1999 16:13:21 GMT Lines: 50 Message-ID: <37a866a1$0$13652@nntp1.ba.best.com> NNTP-Posting-Host: fpage2.ba.best.com X-Trace: nntp1.ba.best.com 933783201 13652 alanjohn@206.86.8.18 Xref: biosci bionet.general:33529 bionet.software:23924 bionet.info-theory:7219 bionet.molec-model:2648 bionet.cellbiol:12235 bionet.molbio.methds-reagnts:77887 bionet.molbio.proteins:14655 bionet.plants:22440 bionet.plants.education:5359 There is a new web portal for all things related to molecular biology and bioinformatics (including the related fields of cell biology, biochemistry, genetics, genomics, XXX). Currently www.MolBio.org provides a news service where the web community can post information related to molecular biology (et al.) and bioinformatics. In addition to the news service, www.MolBio.org provides spam free discussion groups. Do you have information to share such as: - Conference - Press Release - Course - Protocol - News Bite - Software - Research Finding - Tip - Database - Web Site - FTP Site - Web Based Program/Tool - Mailing List - Other Related to the fields of: - Biochemistry - Biotechnology/Biotech - Cell Biology - Computational Biology - Genetics - Genomics - Molecular Biology - Other Then please submit it to www.MolBio.org via the news form at http://www.molbio.org/postnews.cgi. The more info you post, the more useful www.MolBio.org will be. The information you post doesn't need to originate from yourself -- it can be anything you come across in searching the web, reading a journal, browsing bionet, etc... If in doubt, post it! If you have any questions, comments, or requests -- feel free to contact me at Alan@MolBio.org. Thanks, Alan Williams www.MolBio.org ps -- www.MolBio.org is loosly setup as a slashdot (www.slashdot.org) for biology. Follow-ups have been directed to bionet.general I seem to be having problems with UCR's news server, so my apologies if multiple posts show up. ************************************************************************ Alan Williams ------------------------------------------------------------------------ University of California, Riverside "Where observation is concerned, Dept. of Botany and Plant Sciences chance favors the prepared mind." Alan@MolBio.org -- Louis Pasteur ************************************************************************ From owner-software@net.bio.net Wed Aug 04 16:11:00 1999 Path: biosci!ms.bd.com!Bill_A_Nussbaumer From: Bill_A_Nussbaumer@ms.bd.com Newsgroups: bionet.software Subject: Re: Free sequence conversion software? Date: 4 Aug 1999 10:10:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <852567C3.00578882.00@7crmta_md.ms.bd.com> NNTP-Posting-Host: net.bio.net Bill A Nussbaumer@BDX 08/04/99 01:03 PM Perhaps you could try the free program on this web page. I've never tried it so I can say nothing about it, but it might be worth a quick look. It's Win9X/NT software by the way. http://www.genestudio.com/seqverter.htm Bill Nussbaumer I hope this question is not too boring, but I'm looking for tool to convert data in EMBL feature table (FT) format to GenBank format. Is there anything free I could ask my UNIX administrator to install? I would appreciate any helpful hints. Frank From owner-software@net.bio.net Wed Aug 04 16:47:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news-out.uswest.net!news.uswest.net!not-for-mail Message-ID: <37A87A73.8BFC88A8@bioreason.com> From: Andrew Dalke Organization: Bioreason, Inc. X-Mailer: Mozilla 4.05C-SGI [en] (X11; U; IRIX64 6.5 IP30) MIME-Version: 1.0 Newsgroups: bionet.software Subject: Re: unBLASTable sequence? References: <37A74013.61AEDC92@icr.ac.uk> <7o8sm5$do2$1@news.u-strasbg.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 30 Date: Wed, 04 Aug 1999 11:37:55 -0600 NNTP-Posting-Host: 207.108.245.3 X-Trace: news.uswest.net 933788438 207.108.245.3 (Wed, 04 Aug 1999 12:40:38 CDT) NNTP-Posting-Date: Wed, 04 Aug 1999 12:40:38 CDT Francois Jeanmougin > It is filtered due to its low complexity. Removing the > filters as suggested by Andrew will "flood" your output with lot of > poly-prolines sequences, with no biological means nor informations. In many cases, yes, but there have been a few times where I didn't get any hits with filtering turned on, and some, about 5 or so, hits with filtering turned off. As for the *relevancy* of the results, that's a whole 'nother issue :) For example -- example since I don't remember the details of the original circumstances -- suppose you are looking for some somewhat homologous sequence in the PDB so you can get a couple of templates to mutate for the construction of a structure prediction. All you want are some rough ideas to use as the basis of the prediction. Filtering out low-complexity sequences could make it so you have no hits, whereas without a filter you might get some hits and be able to use the corresponding structure as a template. Of course, odds are that the structure will be random coil, but I'll bet that some of the low-complexity sequences have a pretty well defined structure; and I'll bet that SEG doesn't take structural aspects into account. But I could be wrong. Hmm, there's a project for someone :) Andrew Dalke dalke@bioreason.com From owner-software@net.bio.net Wed Aug 04 19:24:00 1999 Path: biosci!ms.bd.com!Bill_A_Nussbaumer From: Bill_A_Nussbaumer@ms.bd.com Newsgroups: bionet.software Subject: Re: unBLASTable sequence?- additional question Date: 4 Aug 1999 13:24:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <852567C3.00695290.00@7crmta_md.ms.bd.com> NNTP-Posting-Host: net.bio.net Bill A Nussbaumer@BDX 08/04/99 04:17 PM I hope I'm not hi-jacking this post, but I'm somewhat unfamiliar with the topic and have been following along. Could someone explain to me what exactly defines a "low complexity" protein sequence. Is it just the short length or the repetitious nature of the amino acids contained? Much appreciated, Bill Nussbaumer From owner-software@net.bio.net Wed Aug 04 21:55:00 1999 Path: biosci!MAILCITY.COM!user5621 From: user5621@MAILCITY.COM Newsgroups: bionet.software Subject: ADV:What you don't know about your money will hurt you Date: 4 Aug 1999 15:55:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <989.283923.245949.user5621@mailcity.com> NNTP-Posting-Host: net.bio.net ...................................... This is a one time mailing, no need to be removed. ...................................... What you don't know about your money will hurt you!! Millions of people make huge financial decisions every day. These decisions mold our financial well being. These same decisions can bring us financial freedom or financial defeat. What we are trying to do is to change the way you look at your money. Your money needs to work for you since you work so hard for your money. 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From owner-software@net.bio.net Thu Aug 05 00:17:00 1999 Path: biosci!biosci!not-for-mail From: Kim Rutherford Newsgroups: bionet.software Subject: First release of Artemis - A DNA sequence annotation tool Date: 4 Aug 1999 18:16:50 -0700 Organization: The Sanger Centre Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: kmr+news@sanger.ac.uk NNTP-Posting-Host: net.bio.net The Sanger Centre is pleased to announce the availability of the first release of Artemis. Artemis is a free DNA sequence viewer and annotation tool which is capable of reading and writing complete EMBL entries. Documentation, screenshots and download instructions for Artemis are available from: http://www.sanger.ac.uk/Software/Artemis/ Description =========== Artemis is a DNA sequence viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, reads EMBL-format sequences and feature tables, and can work on sequences of any size from a few kb to entire genomes of 5 Mb or more. Artemis distribution ==================== Artemis may be freely distributed under the terms of the GNU General Public License, and should run on any system with a recent version of Java, but it is currently best supported on UNIX. Please note that, although we believe Artemis to be useful in its present form, it is still undergoing continuous testing and development. Mailing list ============ We welcome contributions to Artemis and suggestions for new features. An email discussion list has been set up for this purpose. To join, send a message to 'majordomo@sanger.ac.uk' with 'subscribe artemis' in the body (not the subject). Announcements will also be sent to this list. Acknowledgments =============== The development of Artemis is funded by the Wellcome Trust's Beowulf Genomics initiative, through its support of the Pathogen Sequencing Unit. From owner-software@net.bio.net Thu Aug 05 06:05:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!grolier!ciril.fr!news.u-strasbg.fr!not-for-mail From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: unBLASTable sequence?- additional question Date: 5 Aug 1999 08:02:02 GMT Organization: CRC - Universite Louis Pasteur Strasbourg France Message-ID: <7obgdq$eck$1@news.u-strasbg.fr> References: <852567C3.00695290.00@7crmta_md.ms.bd.com> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.u-strasbg.fr 933840122 14740 130.79.79.13 (5 Aug 1999 08:02:02 GMT) X-Complaints-To: usenet@u-strasbg.fr NNTP-Posting-Date: 5 Aug 1999 08:02:02 GMT X-Newsreader: knews 1.0b.0 Mail-Copies-To: never Lines: 42 In article <852567C3.00695290.00@7crmta_md.ms.bd.com>, Bill_A_Nussbaumer@ms.bd.com writes: > I hope I'm not hi-jacking this post, but I'm somewhat unfamiliar with the topic > and have been following along. Could someone explain to me what exactly defines > a "low complexity" protein sequence. Is it just the short length or the > repetitious nature of the amino acids contained? According to : http://www.ncbi.nlm.nih.gov/BLAST/blast_FAQs.html#LCR whose english is much more understandabel : <> Much more details in Methods Enzymol 1996;266:554-71 I think. Filers used by blast are Seg/Xnu or Dust. You could probably find the corresponding documentation around on NCBI site. Seg for proteins and Dust for nucleotides. See the "Filter" section of : http://www.ncbi.nlm.nih.gov/BLAST/blast_help.html Anyway, this one more euristic added to Blast, as pointed by Andrew this could be sometimes unappropriate. Such sequence could be statistically unusable or should be analyzed by other means. François. From owner-software@net.bio.net Thu Aug 05 12:16:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!easynet-tele!easynet.net!news.vas-net.net!server2.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Alessandro Guffanti Newsgroups: bionet.software Subject: Re: unBLASTable sequence? Date: Thu, 05 Aug 1999 14:08:41 +0100 Organization: The Sanger Centre Lines: 69 Message-ID: <37A98CD9.45112310@sanger.ac.uk> References: <37A74013.61AEDC92@icr.ac.uk> NNTP-Posting-Host: caldy.sanger.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 933858521 19531 193.60.84.232 (5 Aug 1999 13:08:41 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 5 Aug 1999 13:08:41 GMT X-Mailer: Mozilla 4.08 [en] (X11; I; OSF1 V4.0 alpha) Hallo Kenny. You sequence is a classic example of "repetitive" or "low entropy" region which is filtered away by specific programs *before* the actual Blast database search takes place. This is to avoid too many spurious matches in your output, for reasons which you may find explained below for what pertains protein seqs. There is always a way to turn this filtering option off and it is suggested you try and search also with the unfiltered sequence. Best Wishes, Alessandro. Paraic Kenny wrote: > Hi all, > > I was trying to BLAST a protein sequence today at the NCBI blast server > and in the results, part of my query sequence came up as a row of > XXXXXXXXs even though it is directly identical to a sequence in the > databases. > Interspersed local regions of very simple amino acid composition are > surprisingly abundant in protein sequences. These regions include different > types of residue clusters, some of which contain homopolymers, short period > repeats or a periodic mosaic of a few residue types. More than half of the > sequences in the database contain at least one such region, and 14% of the > amino acids occur in clusters of highly biased composition, called > "low-complexity regions" (for a review, see Wootton, J. & Federhen, S. > Computers Chem. 17, 149-163 ). > Low complexity segments confound database search algorithms in two ways. > First, most of these segments do not generally give meaningful alignments > in ways that reflect actual structure and mutational history: they > evidently evolved relatively rapidly by processes such as replication > slippage and repeat expansion. Second, the residue composition of > low-complexity segments is very different from that of the database as a > whole. This is evident if all low-complexity segments in the database are > grouped into a single class: a strong excess of alanine, glycine, proline, > serine, glutamate and glutamine results. These statistical biases contrast > with those that charachterize the bulk of most query and database > sequences, and on which score-based alignment statistics are founded. Thus > the high scores of alignments of low-complexity segments are due primarily > to their compositional biases and do not necessarily reflect significant > position similarity. > In the case of programs for database search by homology, the presence of > low complexity regions or of repetitive segments in your query sequence > causes an enormous output or the output size limits can cut off your output > long before all the significative segments are displayed. You can avoid > this by choosing one of the protein filters SEG (eliminates low-complexity > regions from your query sequence) or XNU (eliminates statistically > significant short tandem repeats). The ALU-Protein filter eliminates > eventual Alu sequences present in your protein. The presence of Alu > elements in coding regions has been a controversial issue for sometime, but > it seems established that sequences containing such elements come from > cloning artifacts or, more rarely, expressed pseudogenes (Claverie,J.-M. & > Makalowsky, W. Nature 371, 752). So, if the filtering highlights the > presence of an ALU repeat in the coding part of your sequence, you should > be extremely cautious with your data. > -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Alessandro Guffanti - Informatics The Sanger Centre, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA, United Kingdom phone: +1223-834244 * fax: +1223-494919 http://www.sanger.ac.uk/Users/ag3 From owner-software@net.bio.net Thu Aug 05 16:16:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!arclight.uoregon.edu!wn4feed!worldnet.att.net!128.230.129.106!news.maxwell.syr.edu!nntp2.deja.com!nnrp1.deja.com!not-for-mail From: piotrk@ibb.waw.pl Newsgroups: bionet.software Subject: Re: [Announce] www.MolBio.org -- New Biology Portal Date: Thu, 05 Aug 1999 16:55:33 GMT Organization: Deja.com - Share what you know. Learn what you don't. Lines: 21 Message-ID: <7ocflu$ilm$1@nnrp1.deja.com> References: <37a866a1$0$13652@nntp1.ba.best.com> NNTP-Posting-Host: 212.87.28.79 X-Article-Creation-Date: Thu Aug 05 16:55:33 1999 GMT X-Http-User-Agent: Mozilla/4.61 [en] (X11; I; Linux 2.2.5 i586) X-Http-Proxy: 1.0 arete.ibb.waw.pl:3128 (Squid/2.0.PATCH2), 1.0 x26.deja.com:80 (Squid/1.1.22) for client 212.87.28.76, 212.87.28.79 X-MyDeja-Info: XMYDJUIDpiotrkozbial [...] > www.MolBio.org is loosly setup as a slashdot (www.slashdot.org) > for biology. [...] I am sure that you have not seen slashdot-like "BioPL". The only difference: BioPL it is a discussion forum about current topics in bioinformatics and biological sciences. Best regards Piotr BioPL: http://arete.ibb.waw.pl/html/news/ P.S.You can click the Eglish flag to get a list of all articles in English. Sent via Deja.com http://www.deja.com/ Share what you know. Learn what you don't. From owner-software@net.bio.net Thu Aug 05 19:22:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!ihug.co.nz!not-for-mail From: "Marcel Dinger" Newsgroups: bionet.software Subject: Re: Web sites for PCR primer design Date: Fri, 6 Aug 1999 08:09:08 +1200 Organization: Genamics Lines: 35 Message-ID: <933884189.942479@ham.ihug.co.nz> References: <7o819c$o8r$1@green.kreonet.re.kr> Reply-To: "Marcel Dinger" NNTP-Posting-Host: ham.ihug.co.nz X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Cache-Post-Path: ham.ihug.co.nz!unknown@p13-max6.ham.ihug.co.nz X-Cache: nntpcache 2.3.3 (see http://www.nntpcache.org/) Hi, You could try some of the online tools available in the PCR section at Genamics SoftwareSeek. The URL is http://genamics.com/software/ Hope this helps. Marcel Dinger, Genamics. > Hi, > > Does anyone know the web site for PCR primer design? > > I have been using http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi > > primer 3 service but sometimes I found that the resulting primer was dimeric > > configuration. Please tell me the annother site for PCR primer design. > > -- > ___________________________________________________________________________ > > Ajou medical school Dooyeon Kim ...................... > Pharmacology Lab. dykim@bioneer.kaist.ac.kr > ___________________________________________________________________________ > From owner-software@net.bio.net Thu Aug 05 21:02:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!join.news.pipex.net!pipex!warm.news.pipex.net!pipex!krypton.inbe.net!INbe.net!not-for-mail From: robertc@mail.kinetic.be (robert) Newsgroups: bionet.software Subject: SuperBase Date: Thu, 05 Aug 1999 21:57:18 GMT Organization: UUNET Benelux (post does not reflect views of UUNET Benelux) Lines: 3 Message-ID: <37ab0884.2975766@news.kinetic.be> NNTP-Posting-Host: 194.7.176.216 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent 1.5/32.452 Where can I find Superbase-prog Txs robertc@mail.kinetic.be From owner-software@net.bio.net Fri Aug 06 03:15:00 1999 Path: biosci!rutgers!uwm.edu!arclight.uoregon.edu!logbridge.uoregon.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Free sequence conversion software? Date: 6 Aug 1999 04:09:01 GMT Organization: Biology, Indiana University - Bloomington Lines: 12 Message-ID: <7odn4t$akt$1@jetsam.uits.indiana.edu> References: <37A86595.150E0918@Genetik.Uni-Bielefeld.DE> NNTP-Posting-Host: chipmunk.bio.indiana.edu If time permits, I'll have an updated readseq that does feature table and documentation conversions (among genbank embl and xml variants) next week. Keep tuned in here, or peek at http://iubio.bio.indiana.edu/soft/molbio/readseq/ - Don ps., this version is written in java, so will run on any java-capable os. -- -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu From owner-software@net.bio.net Fri Aug 06 14:27:00 1999 Path: biosci!CITYDESK.CO.UK!nue87 From: nue87@CITYDESK.CO.UK (mon14wes) Newsgroups: bionet.software Subject: Thank You for visiting Atlantic Office Service & Supplies, Inc. Date: 6 Aug 1999 08:27:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <199908061162JAA34692@yervceso.univ-aix.fr> NNTP-Posting-Host: net.bio.net Thank You for visiting Atlantic Office Service & Supplies, Inc. Atlantic Office Service & Supplies, Inc. is here to serve you the customer with over 25,000 office supplies, faciltity items, and furniture products, with nationwide delivery to your door! FREE shipping & FREE gift with all $50.00 orders or more! For info email: dagnabit1@bigfoot.com with subject office for removal email: dagnabit1@bigfoot.com with subject remove 0 From owner-software@net.bio.net Fri Aug 06 15:40:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!howland.erols.net!news-out-b.news.pipex.net.MISMATCH!tank.news.pipex.net!pipex!uunet!ams.uu.net!ffx.uu.net!newsfeed.attap.net!infeed.jaring.my!not-for-mail From: "Venson Yap" Newsgroups: bionet.software Subject: identical pc id Date: Sat, 7 Aug 1999 00:41:22 +0800 Organization: Unconfigured Lines: 3 Message-ID: <7of2qd$cfb$1@news6.jaring.my> NNTP-Posting-Host: j60.dms33.jaring.my X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 what computer system that provide personal pc id? From owner-software@net.bio.net Fri Aug 06 18:17:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newsfeed.berkeley.edu!easynet-fr!buggy.easynet.fr!not-for-mail From: philimar@easynet.fr (Philippe Marquis) Newsgroups: bionet.software Subject: method validator software Date: Fri, 06 Aug 1999 19:17:54 GMT Organization: [Posted via] Easynet France Lines: 30 Message-ID: <37ab3480.328801@news.easynet.fr> NNTP-Posting-Host: 212.180.8.193 X-Trace: buggy.easynet.fr 933966661 14291 212.180.8.193 (6 Aug 1999 19:11:01 GMT) X-Complaints-To: abuse@easynet.fr NNTP-Posting-Date: 6 Aug 1999 19:11:01 GMT X-Newsreader: Forte Free Agent 1.11/32.235 First release of a new free software : Method Validator Win 95/98/NT4 Method validator is a statistical programme designed for comparing analytical techniques in clinical laboratories. Its aim is to provide a simple tool which can be used intuitively without any training. It makes use of conventional statistical techniques : - Difference plot (with or without log transformation). - Normal linear regression (weighted or unweighted). - Deming regression (weighted or unweighted). - Passing and Bablok non-parametric methods (comparison test and estimation of the regression). The graphical tools have been studied in depth to simplify the plotting of data. Import/export functions are provided to allow exchange of data with a spreadsheet or copy/pasting of the graphs in a word processor. A random number generator allows various experimental situations to be simulated by changing the analytical CV of each method and the distribution of data. URL to download: http://perso.easynet.fr/~philimar Philippe Marquis MD Centre hospitalier Metz - France philimar@easynet.fr From owner-software@net.bio.net Fri Aug 06 19:17:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!newsswitch.lcs.mit.edu!newspump.monmouth.com!newspeer.monmouth.com!tank.news.pipex.net!pipex!newsfeed.nacamar.de!newsfeed.nacamar.de!newscore.gigabell.net!newscore.ipf.de!newsfeed00.btx.dtag.de!newsfeed01.btx.dtag.de!newsmm00.btx.dtag.de!news.btx.dtag.de!not-for-mail From: "Prinz Igor" Newsgroups: bionet.software Subject: paint shop pro Date: Fri, 6 Aug 1999 22:06:37 +0200 Organization: T-Online Lines: 7 Message-ID: <7offce$2mv$1@news05.btx.dtag.de> Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news05.btx.dtag.de 933970126 2783 320055114984-0001 990806 20:08:46 X-Complaints-To: abuse@t-online.de X-Sender: 320055114984-0001@t-online.de X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Hi, I' m looking for paint shop pro 5.01 evaluation. Important it must be the english version. perhaps you can help me ?! Thank you. From owner-software@net.bio.net Fri Aug 06 20:51:00 1999 From: (Heiko Tietze) Newsgroups: bionet.software Subject: Re: paint shop pro Date: Fri, 06 Aug 1999 21:45:07 GMT Message-ID: <37ad575f.44911769@news.uni-wuerzburg.de> References: <7offce$2mv$1@news05.btx.dtag.de> X-Newsreader: Forte Agent 1.5/32.452 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: wy3dh0.psychologie.uni-wuerzburg.de Lines: 2 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!209.50.235.254!europa.netcrusader.net!192.148.253.68!netnews.com!newspeer.monmouth.com!uni-erlangen.de!uni-wuerzburg.de!wy3dh0.psychologie.uni-wuerzburg.de www.jasc.com ICQ: 38076460 From owner-software@net.bio.net Fri Aug 06 20:56:00 1999 Path: biosci!newshost.lanl.gov!arclight.uoregon.edu!wn4feed!worldnet.att.net!128.230.129.106!news.maxwell.syr.edu!howland.erols.net!news-out.digex.net.MISMATCH!dca1-hub1.news.digex.net!dca1-feed4.news.digex.net!intermedia!news1.bms.com!not-for-mail From: A John Watson Newsgroups: bionet.software Subject: Re: Web sites for PCR primer design Date: Fri, 06 Aug 1999 17:40:54 -0400 Organization: Bristol-Myers Squibb Company Lines: 34 Message-ID: <37AB5666.5AC45137@bms.com> References: <7o819c$o8r$1@green.kreonet.re.kr> NNTP-Posting-Host: newsreader-hpw1.net.bms.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en]C-BMY (WinNT; U) X-Accept-Language: en Cache-Post-Path: newsreader-hpw1.net.bms.com!unknown@priwfda0634043.wfd.pri.bms.com X-Cache: nntpcache 2.3.3 (see http://www.nntpcache.org/) There was a review of several web-based primer designers. http://www.alkami.com/primers/refdsgn.htm Cheers, John Watson Bristol-Myers Squibb Lead Discovery watosnja@bms.com ****************************************************************** If you're not part of the solution, you're part of the precipitate ****************************************************************** Dooyeon Kim wrote: > > Hi, > > Does anyone know the web site for PCR primer design? > > I have been using http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi > > primer 3 service but sometimes I found that the resulting primer was dimeric > > configuration. Please tell me the annother site for PCR primer design. > > -- > ___________________________________________________________________________ > > Ajou medical school Dooyeon Kim ...................... > Pharmacology Lab. dykim@bioneer.kaist.ac.kr > ___________________________________________________________________________ > From owner-software@net.bio.net Fri Aug 06 22:43:00 1999 From: caboo@aol.com Newsgroups: bionet.software,bit.listserv.ada-law,bit.listserv.aix-l Subject: just for adults 24361 Message-ID: <06089916.3924@aol.com> Date: Friday, 06 Aug 1999 16:39:24 -0600 Organization: FREE TEENS Reply-To: jimmyzfish@aol.com NNTP-Posting-Host: news.uncensored-news.com Lines: 12 X-Complaints-To: abuse@uncensored-news.com Path: biosci!rutgers!nntp.upenn.edu!newsserver.jvnc.net!198.138.0.5!newshub.northeast.verio.net!newspeer.monmouth.com!news.ruhrgebiet.individual.net!feed.newsfeeds.com!newsfeeds.com!news.planetc.com!news.uncensored-news.com!news.uncensored-news.com Adults Only: http://207.240.225.250 X)3-AF_+ {}{}{} Posted via Uncensored-News.Com, http://www.uncensored-news.com {}{}{} {}{}{}{} Only $8.95 A Month, - The Worlds Uncensored News Source {}{}{}{} {}{}{}{}{} Five News Servers with a BINARIES ONLY Server {}{}{}{}{} From owner-software@net.bio.net Sat Aug 07 09:44:00 1999 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!dispose.news.demon.net!demon!newsfeed.nacamar.de!newsfeed.nacamar.de!fu-berlin.de!kassandra.civilserve.COM!not-for-mail From: Andrea Hansen Newsgroups: bionet.software Subject: Re: Plasmid drawing packages Date: Sat, 07 Aug 1999 12:37:46 +0200 Organization: TU Braunschweig Message-ID: <37AC0C7A.A1E6F0C8@tu-bs.de> References: <37A5C88F.F7D3A3C5@bbsrc.ac.uk> NNTP-Posting-Host: kassandra.civilserve.com (195.122.146.151) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Access: 16 [4974] X-Trace: fu-berlin.de 934022272 28336 (none) 195.122.146.151 X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.0.36 i586) X-Accept-Language: en Lines: 21 Aedin Culhane wrote: > I have seen commercial programs like Clonemap which seem very nice, but > really need a freeware/shareware plasmid drawing package. I have tried > pDraw32 and Plasmid Processor Pro, but neither seem to produce colour > graphics (in my hands). > I am grateful for any help > Aedin maybe you can find something here: http://www.bioinformatik.de/cgi-bin/browse/Catalog/Software/Unix/ Andrea Hansen Institut fuer Genetik Tel : ++49-531-391-5783 TU Braunschweig Fax : ++49-531-391-5765 Spielmannstr. 7 email : webmaster@bioinformatik.de 38106 Braunschweig http://www.bioinformatik.de From owner-software@net.bio.net Sat Aug 07 11:37:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.nacamar.de!newsfeed.nacamar.de!fu-berlin.de!kassandra.civilserve.COM!not-for-mail From: Andrea Hansen Newsgroups: bionet.software Subject: Re: Web sites for PCR primer design Date: Sat, 07 Aug 1999 14:31:26 +0200 Organization: TU Braunschweig Lines: 19 Message-ID: <37AC271D.80053B66@tu-bs.de> References: <7o819c$o8r$1@green.kreonet.re.kr> NNTP-Posting-Host: kassandra.civilserve.com (195.122.146.151) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Access: 16 [4974] X-Trace: fu-berlin.de 934029090 2537 (none) 195.122.146.151 X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.0.36 i586) X-Accept-Language: en Dooyeon Kim wrote: > Does anyone know the web site for PCR primer design? > Take a look at this site http://www.bioinformatik.de/cgi-bin/browse/Catalog/PCR/ Andrea Hansen Institut fuer Genetik Tel : ++49-531-391-5783 TU Braunschweig Fax : ++49-531-391-5765 Spielmannstr. 7 email : webmaster@bioinformatik.de 38106 Braunschweig http://www.bioinformatik.de From owner-software@net.bio.net Sat Aug 07 15:01:00 1999 Path: biosci!SURFREE.COM!3U35Al7Fo From: 3U35Al7Fo@SURFREE.COM Newsgroups: bionet.software Subject: LET MASS E-MAILING WORK FOR YOU! GET EXPOSED$$$ Date: 7 Aug 1999 09:01:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <199908071553.LAA28663@equinox.shaysnet.com> Reply-To: ju7676767@surfree.com NNTP-Posting-Host: net.bio.net This is Cybernet Enterprise and we are sending you this e-mail to let you in on some of the best prices in Bulk E-Mailing. If you are interested in more information . Please call anytime 209-699-3628 Prices: $200.00 For 1 Million E-Mails Sent. $400.00 For 3 Million E-Mails Sent. $600.00 For 5 Million E-Mails Sent. $800.00 For 7 Million E-Mails Sent. $1000.00 For 10 Million E-Mails Sent. We also have target lists..Just call and ask! P.S. I am able to send you proof of your mailings. I will send you via e-mail, uploaded mail-log files of the actual sendings so you can know first-hand exactly what i'm doing for you. IT REALLY DOES WORK!! I made this ad short so call for more info.. cybernet101@bigfoot.com or e-mail us your name and phone #. If the e-mail link fails please call for more info. From owner-software@net.bio.net Sat Aug 07 16:37:00 1999 Message-ID: <37AC6D62.C86F3AE1@civilserve.com> Date: Sat, 07 Aug 1999 19:31:14 +0200 From: Olaf Ramge Organization: Olaf Ramge X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.0.36 i586) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software Subject: bioinformatik.de Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable NNTP-Posting-Host: 195.122.146.151 X-Trace: 7 Aug 1999 19:18:23 +0100, 195.122.146.151 Lines: 14 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!newsfeed.nacamar.de!blackbush.xlink.net!news-in.ivm.net!hedwik.mik.net!195.122.146.151 Hi, we have a yahoo like Webcatalog with links to bioinformatic-related sites. Because of the high amount of foreign visitors we have decided to translate the categories to english. Any suggestions? Olaf -- = Civilserve =B7 Internetconsulting Am Buergerpark 6 =B7 D-38102 Braunschweig Tel: +49 (0)531-2702126 Fax: +49 (0)531-2702125 eMail: webinfo@civilserve.com =B7 Internet: http://www.civilserve.com From owner-software@net.bio.net Sat Aug 07 16:40:00 1999 Message-ID: <37AC6E18.AB602E60@civilserve.com> Date: Sat, 07 Aug 1999 19:34:16 +0200 From: Olaf Ramge Organization: Olaf Ramge X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.0.36 i586) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software Subject: http://www.bioinformatik.de References: <37AC6D62.C86F3AE1@civilserve.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: 195.122.146.151 X-Trace: 7 Aug 1999 19:21:25 +0100, 195.122.146.151 Lines: 2 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.nacamar.de!newsfeed.nacamar.de!blackbush.xlink.net!news-in.ivm.net!hedwik.mik.net!195.122.146.151 http://www.bioinformatik.de From owner-software@net.bio.net Sat Aug 07 19:04:00 1999 Path: biosci!THEHEADOFFICE.COM!1895permo From: 1895permo@THEHEADOFFICE.COM Newsgroups: bionet.software Subject: The Internet Spy And You! Date: 7 Aug 1999 13:04:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 170 Sender: daemon@net.bio.net Distribution: world Message-ID: <199908071937.MAA11580@cello.stylus.net> NNTP-Posting-Host: net.bio.net Please see disclaimers at the end of this mailing. "THE INTERNET SPY" WE SHOW YOU HOW TO GET THE FACTS ON ANYONE! CONFIDENTIAL The SOFTWARE They Want BANNED In  all 50 STATES. Why? Because these secrets were never intended to reach your eyes... Get the facts on anyone using the Internet! Locate Missing Persons, find Lost Relatives, obtain Addresses 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! 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From owner-software@net.bio.net Sun Aug 08 10:22:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!feed1.news.rcn.net!rcn!cpk-news-hub1.bbnplanet.com!news.gtei.net!firehose.mindspring.com!not-for-mail From: john_q_barlow@hotmail.com (John Barlow) Newsgroups: bionet.software Subject: Re: bioinformatik.de Date: 8 Aug 1999 11:16:42 GMT Organization: MindSpring Enterprises Lines: 30 Message-ID: <7ojouq$dh3$1@nntp9.atl.mindspring.net> References: <37AC6D62.C86F3AE1@civilserve.com> NNTP-Posting-Host: d1.56.4a.22 Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.9 (Released Version) (x86 32bit) Hi: Good start. Your site looks very nice. You can pick-up additional links and ideas from the following catalogs of biosoftware: http://corba.ebi.ac.uk/BioCatalog/ http://www.arc.unm.edu/~aroberts/main/free.htm http://www.eur.nl/FGG/CH1/software.html I hope that other BioNet visitors will add more links to your site. John (Please note that you left some German text on the English pages.) In article <37AC6D62.C86F3AE1@civilserve.com>, o.ramge@civilserve.com says... > >Hi, >we have a yahoo like Webcatalog with links to bioinformatic-related >sites. >Because of the high amount of foreign visitors we have decided to >translate the categories to english. >Any suggestions? > >Olaf >-- = > >Civilserve =B7 Internetconsulting >Am Buergerpark 6 =B7 D-38102 Braunschweig >Tel: +49 (0)531-2702126 Fax: +49 (0)531-2702125 >eMail: webinfo@civilserve.com =B7 Internet: http://www.civilserve.com From owner-software@net.bio.net Mon Aug 09 13:41:00 1999 Path: biosci!MERCURY.TREAD.IT!ziseugo43 From: ziseugo43@MERCURY.TREAD.IT (coubihs) Newsgroups: bionet.software Subject: ..Internet..Company..Makes Pre IPO.Offer Date: 9 Aug 1999 07:41:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 53 Sender: daemon@net.bio.net Distribution: world Message-ID: <19990809881TAA45123@uymois.upm.edu.my> NNTP-Posting-Host: net.bio.net Internet E-commerce companies are hot!! 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This offer is being made under an exemption under the provisions of The Securities Act of 1933-1934, as amended. 1564a64y-1s5646m1a6er =h From owner-software@net.bio.net Mon Aug 09 20:32:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!isdnet!newsfeed.tli.de!newscore.gigabell.net!newscore.ipf.de!news-fra1.dfn.de!aconews.univie.ac.at!news.univie.ac.at!not-for-mail From: "Kirsten Peter Rabitsch" Newsgroups: bionet.software Subject: Re: Batch BLAST Date: Mon, 9 Aug 1999 23:23:23 +0200 Organization: Vienna University, Austria Lines: 20 Message-ID: <7onh1b$h3k$1@www.univie.ac.at> References: <8E13CADBBlidongglobalservenet@news.globalserve.net> NNTP-Posting-Host: uvo-19.univie.ac.at X-Trace: www.univie.ac.at 934233963 17524 131.130.230.19 (9 Aug 1999 21:26:03 GMT) X-Complaints-To: news-adm@news.univie.ac.at NNTP-Posting-Date: 9 Aug 1999 21:26:03 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Alex Dong Li wrote in msg 8E13CADBBlidongglobalservenet@news.globalserve.net... > Why not use webblast? > It is designed to do so. > The current version runs on unix and windows9x/NT > You can get it from > http://www.genet.sickkids.on.ca/bioinfo_resources/software.html Is there something similar out there for FASTA (seems to work somehow better for me for designing primers to genomic DNA)? OR: Is there some packages for Linux to install FASTA just like mentioned above for BLAST. I only need to search the raw data of the yeast genome which is pretty much settled. Thanx, Kirsten Peter Rabitsch From owner-software@net.bio.net Mon Aug 09 21:43:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!qualcomm.com!news.tamu.edu!news.mty.itesm.mx!pumba!not-for-mail From: "Deilson Elgui de Oliveira" Newsgroups: bionet.software Subject: Re: Web sites for PCR primer design Date: Sun, 8 Aug 1999 14:53:30 -0300 Organization: Universidad de Guadalajara Lines: 31 Message-ID: <7okg97$cle$1@pumba.class.udg.mx> References: <7o819c$o8r$1@green.kreonet.re.kr> NNTP-Posting-Host: 200.145.132.130 X-Trace: pumba.class.udg.mx 934134887 12974 200.145.132.130 (8 Aug 1999 17:54:47 GMT) X-Complaints-To: usenet@pumba.class.udg.mx NNTP-Posting-Date: 8 Aug 1999 17:54:47 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 I recommend Primers!"( http://www.alkami.com/cntprmr.cgi?url=http://www.williamstone.com /primers/javascript/), but you can try another tools listed in http://www.alkami.com/primers/refdsgn.htm Dooyeon Kim escreveu nas notícias de mensagem:7o819c$o8r$1@green.kreonet.re.kr... > Hi, > > Does anyone know the web site for PCR primer design? > > I have been using http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi > > primer 3 service but sometimes I found that the resulting primer was dimeric > > configuration. Please tell me the annother site for PCR primer design. > > -- > ___________________________________________________________________________ > > Ajou medical school Dooyeon Kim ...................... > Pharmacology Lab. dykim@bioneer.kaist.ac.kr > ___________________________________________________________________________ > From owner-software@net.bio.net Mon Aug 09 22:07:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!skynet.be!News.Amsterdam.UnisourceCS!news.otenet.gr!not-for-mail From: "Pliktro Software" Newsgroups: bionet.software Subject: OfficePro. Keep all your Appointments, Tasks, Business Associates, Images etc. Date: Tue, 10 Aug 1999 01:52:06 +0300 Organization: Pliktro Software Lines: 17 Message-ID: <7onmhn$5qf$1@newssrv.otenet.gr> NNTP-Posting-Host: athe530-c089.otenet.gr X-Trace: newssrv.otenet.gr 934239607 5967 195.167.121.217 (9 Aug 1999 23:00:07 GMT) X-Complaints-To: abuse@otenet.gr NNTP-Posting-Date: 9 Aug 1999 23:00:07 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 OfficePro is far from a desktop PIM. Õou can keep all your appointments, write down any task, have an extended database of all your business associates, make email list, print in labels your clients addresses, make direct phone calls from within the program and even group your images either in thumbnailed or in photo album format. Download 20 days trial version of OfficePro from Pliktro Software. Look at http://www.pliktro.gr/English/eofficepro.htm From owner-software@net.bio.net Mon Aug 09 22:37:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.algonet.se!algonet!newsfeed.tli.de!blackbush.xlink.net!EU.net!newssrv.ita.tip.net!i2unix!typhoon.libero.it!not-for-mail Message-ID: <37AF565B.81ADCE35@iol.it> From: Pier X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 Newsgroups: bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.software.srs Subject: get paid to surf Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 12 Date: Tue, 10 Aug 1999 00:29:47 +0200 NNTP-Posting-Host: 212.52.68.181 X-Trace: typhoon.libero.it 934238009 212.52.68.181 (Tue, 10 Aug 1999 00:33:29 MET DST) NNTP-Posting-Date: Tue, 10 Aug 1999 00:33:29 MET DST Organization: [Infostrada S.p.A.] Xref: biosci bionet.software:23956 bionet.software.acedb:2530 bionet.software.gcg:3654 bionet.software.srs:1567 They pay me to surf the Web. They even gave me a browser that has language translation for Web sites built in! It's at: http://www.gotoworld.com/getpaid/default.asp?rid=1017405373 The browser also has all these plug-in for MP3s, Internet Radio stations, and TV. I even downloaded an editor that lets me type in different languages. Have a nice day! From owner-software@net.bio.net Tue Aug 10 07:06:00 1999 From: Cornelius Krasel Subject: Re: Batch BLAST Newsgroups: bionet.software References: <8E13CADBBlidongglobalservenet@news.globalserve.net> <7onh1b$h3k$1@www.univie.ac.at> User-Agent: tin/pre-1.4-19990413 ("Endemoniada") (UNIX) (Linux/2.0.36 (i486)) Date: Tue, 10 Aug 1999 09:39:35 +0200 Message-ID: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de Lines: 14 Path: biosci!rutgers!nntp.upenn.edu!newsserver.jvnc.net!198.138.0.5!newshub.northeast.verio.net!news.maxwell.syr.edu!newsfeed.nacamar.de!uni-erlangen.de!uni-wuerzburg.de!not-for-mail Kirsten Peter Rabitsch wrote: > OR: Is there some packages for Linux to install FASTA just like mentioned > above for BLAST. I only need to search the raw data of the yeast genome > which is pretty much settled. There is a nifty script out there called "mailfasta" which works via email. I am not sure whether that is what you want. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP4 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Tue Aug 10 07:18:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!cgl!itssrv1.ucsf.edu!usenet From: Richard Moore Newsgroups: bionet.software Subject: Re: unBLASTable sequence? Date: Mon, 09 Aug 1999 16:40:56 -0700 Organization: UCSF Lines: 20 Message-ID: <37AF6708.DFD53C62@doppel.ucsf.edu> References: <37A74013.61AEDC92@icr.ac.uk> NNTP-Posting-Host: prion.ucsf.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.5 IP20) X-Accept-Language: en Dear unBLASTable, The bit of your sequence which has been replaced by a row of Xs is either repetitive or of "low complexity". To me this looks like its the case as this part of your sequence has a run of prolines. Try de-selecting this filter by turning off the filter option next time you run blast. Not all web forms for blast give you this option. Try looking around for web sites which give you more control over your search. The NCBI -BLAST site advanced search allows you to turn off this filter. Of course this will result in lots of hits with other proline rich sequences ...just fiddle around with all the options on BLAST until it works the way you want it to. Richard C Moore, PhD Prusiner Lab University of California San Francisco Tel: (415) 502 1949 Fax: (415) 476 8386 From owner-software@net.bio.net Tue Aug 10 12:15:00 1999 Path: biosci!CECALC.ULA.VE!golfredo From: golfredo@CECALC.ULA.VE (Golfredo Catalani) Newsgroups: bionet.software Subject: genetic-programming.com-Home-Page Date: 10 Aug 1999 06:15:45 -0700 Organization: CeCalCULA Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <37B02710.C18F0F60@cecalc.ula.ve> NNTP-Posting-Host: net.bio.net Genetic programming is an automated method for creating a working computer program from a high-level problem statement of a problem. Genetic programming evolves computer programs by genetically breeding a population of computer programs using the principles of Darwinian natural selection and biologically inspired operations. http://www.genetic-programming.com/ From owner-software@net.bio.net Tue Aug 10 13:44:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!cyclone.bc.net!news.maxwell.syr.edu!feed1.news.rcn.net!rcn!sula2 From: sula2@erols.com (Eric Anderson) Newsgroups: bionet.software Subject: Statistics/Graphing Software for Mac Date: Tue, 10 Aug 1999 10:37:50 -0400 Organization: SUNY-Brooklyn Lines: 19 Message-ID: X-Trace: I59Z6hfox2OnZ+gSJNDu1C7IR8A88E7SuiqjTWgQQfk= X-Complaints-To: abuse@rcn.com NNTP-Posting-Date: 10 Aug 1999 14:37:40 GMT X-Newsreader: MT-NewsWatcher 2.3.5 I've been out of the lab for a few years (working on the MD part of my MD/PhD) and so I've lost track of the graphing and statistics programs that people are using on the Mac. We're in need of a basic program something that can do more than Excel and quite a bit less than Statistica. In previous labs I've used Delta Graph (which I can't find anymore), Sigma Plot (which appears to only be available for Windoze now) and Cricket Graph (any program with Cricket in the title is hard to respect and I never liked it anyway). I'm giving GraphPad a shot right now, but any other recommendations, or pointers to Mac Versions of Delta Graph and/or Sigma Plot would be greatly appreciated. Thanks, Eric From owner-software@net.bio.net Tue Aug 10 16:47:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Readseq version 2 (biosequence conversion) available for testing Date: 10 Aug 1999 17:41:18 GMT Organization: Biology, Indiana University - Bloomington Lines: 93 Message-ID: <7opo7u$db$1@flotsam.uits.indiana.edu> NNTP-Posting-Host: chipmunk.bio.indiana.edu Readseq version 2.0j (august 1999) A program to read & reformat biosequences, and a package of methods for programmmers to incorporate into their software for this end. This is version is written in the Java language. This release is available for testing. Some debugging is still needed. Your comments are welcome. Find it at http://iubio.bio.indiana.edu/soft/molbio/readseq/java/, or ftp://iubio.bio.indiana.edu/molbio/readseq/java/ Programs available in the readseq.jar package -------------------- For the current help document, use a Java Runtime command of jre -cp readseq.jar help Graphic interface to Readseq (using Java swing) Usage: jre -cp readseq.jar iubio.readseq.app Macintosh users: See also Readseq.macapp, a small Mac Java application to launch readseq.jar without a jre commandline. HTTP server common gateway interface to Readseq Web servers can run this program to provide biosequence conversion See for example http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi See the help document for usage information Command line version (classic-readseq options are supported) Usage: jre -cp readseq.jar run [options] input-file(s) Options -a[ll] select All sequences -c[aselower] change to lower case -C[ASEUPPER] change to UPPER CASE -degap[=-] remove gap symbols -i[tem=2,3,4] select Item number(s) from several -l[ist] List sequences only -o[utput=]out.seq redirect Output -p[ipe] Pipe (command line, stdout) -t[ranslate=]io translate input symbol [i] to output symbol [o] use several -tio to translate several symbols -v[erbose] Verbose progress -f[ormat=]# Format number for output, or -f[ormat=]Name Format name for output see Formats list below for names and numbers -inform[at]=# input format number, or -inform[at]=Name input format name. Assume input data is this format -ch[ecksum] calculate & print checksum of sequences Pretty format options: -wid[th]=# sequence line width -tab=# left indent -col[space]=# column space within sequence line on output -gap[count] count gap chars in sequence numbers -nameleft, -nameright[=#] name on left/right side [=max width] -nametop name at top/bottom -numleft, -numright seq index on left/right side -numtop, -numbot index on top/bottom -match[=.] use match base for 2..n species -inter[line=#] blank line(s) between sequence blocks This program requires a Java runtime (jre) program, version 1.1.x These options and call format are compatible with the classic readseq (v.1992) with exception of no -reverse option. Known biosequence formats: ID Name Read Write Int'leaf Document 1 IG|Stanford yes yes -- -- 2 GenBank|GB yes yes -- yes 3 NBRF yes yes -- -- 4 EMBL yes yes -- yes 5 GCG yes yes -- -- 6 DNAStrider yes yes -- -- 7 Fitch -- -- -- -- 8 Pearson|Fasta yes yes -- -- 9 Zuker -- -- -- -- 10 Olsen -- -- yes -- 11 Phylip3.2 yes yes yes -- 12 Phylip|Phylip4 yes yes yes -- 13 Plain|Raw yes yes -- -- 14 PIR|CODATA yes yes -- -- 15 MSF yes yes yes -- 16 ASN.1 -- -- -- -- 17 PAUP|NEXUS yes yes yes -- 18 Pretty -- yes yes -- 19 BLAST yes -- yes -- 20 XML yes yes -- yes (Int'leaf = interleaved format; Document = documentation is parsed) -------------------- -- -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu From owner-software@net.bio.net Tue Aug 10 18:39:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newsfeed.icl.net!newsfeed.nacamar.de!newscore.univie.ac.at!aconews.univie.ac.at!news.univie.ac.at!not-for-mail From: "Kirsten Peter Rabitsch" Newsgroups: bionet.software Subject: Re: Batch BLAST Date: Tue, 10 Aug 1999 21:30:17 +0200 Organization: Vienna University, Austria Lines: 16 Message-ID: <7opupg$4hu8$1@www.univie.ac.at> References: <8E13CADBBlidongglobalservenet@news.globalserve.net> <7onh1b$h3k$1@www.univie.ac.at> NNTP-Posting-Host: unet4-22.univie.ac.at X-Trace: www.univie.ac.at 934313584 149448 131.130.233.22 (10 Aug 1999 19:33:04 GMT) X-Complaints-To: news-adm@news.univie.ac.at NNTP-Posting-Date: 10 Aug 1999 19:33:04 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Cornelius Krasel wrote in msg: nvkoo7.ibc.ln@wpxx02.toxi.uni-wuerzburg.de... > There is a nifty script out there called "mailfasta" which works via > email. I am not sure whether that is what you want. Thanx a lot. Got it from ftp://ftp.embl-heidelberg.de/pub/software/unix/ See README for information. Haven't tried it yet (don't have a unix maschine at home). Peter From owner-software@net.bio.net Tue Aug 10 19:15:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newsfeed.icl.net!newsfeed.icl.net!nntp.news.xara.net!xara.net!server6.netnews.ja.net!server4.netnews.ja.net!news.icnet!not-for-mail From: Arne Mueller Newsgroups: bionet.software Subject: Re: Database integration with sequence analysis software - how? Date: Tue, 10 Aug 1999 20:45:43 +0100 Organization: Imperial Cancer Research Fund Lines: 89 Message-ID: <37B08167.9F6F83A7@icrf.icnet.uk> References: <37825578.A352B0CC@ibb.waw.pl> NNTP-Posting-Host: jumbo.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5C-SGI [en] (X11; I; IRIX64 6.5 IP25) X-Accept-Language: en To: piotrk@ibb.waw.pl Piotr Kozbial wrote: > > I am interested in testing several ideas about organization of genomic > information. > > Could you please send me references about: > > 1. Sequences management in relational databases. Hi, I think storing sequence data with all the known biological information in a relational SQL database must be be far more efficient than anything else... However smart database design seems to be a tricky thing and bioscientists like me like the old text formated files, also portability is easy using these flat. text files. However I decided to use an SQL database to manage all my sequence data plus all the additional stuff connected to the sequences. > Databases, I know, store data in tables and rows, but sequences seems to > be stored in flat files (i.e. in FASTA format). Is it good idea to chop > the sequences and transfer them into relational database? Some kinds of > sequences are well suited for storage in relational database (i.e. > protein and cDNA sequences), but genomic sequences are not. Is it good > idea to cut genomic sequences into fragments containing ORFs with > theirs upstream and downstream sequence, and with some positioning > information (i.e.. IDs of upstream and downstream ORFs). With each ORF > in the database it is possible to store additional information (computed > or taken from known literature) like: Hm, if the genome identification is complete I'd say yes, split the genome into ORFs including all the positioning data, regulatory elements (if known) etc. . I know not much about relational databases but it seems to be a (biological) problem splitting the data and than connecting it again when searching the database. Honestly - I've no idea about THE ideal solution, so I'd split the data! > -cDNA sequence, > -IDs of known aa motives, > -ID of known conserved structural domains, > -ID of interacting proteins, > -pre computed information about structural, sequence, and functional > homologies (similar to "neighbors" in NCBI databases), > -all other information (especially raw experimental data), > > 2. There are lots of tools for sequence analysis written in perl, c, > c++, etc. > How the interface between the database and the tools should be designed? > Are there any examples? I'd use some software in the middle. You may need a tool that performes the sql database query and writes the sequences (results) in a common format (e.g. fasta) to a your whatever program (Fasta, Blast ...), otherwise you've to hack the code of the existing programs you use. HTTP-saervers and databases work together via cgi-scripts, there are lots of intermediate software packages that are intended to make live easier to communicate between applications and database-servers. If you're interested in MySQL and related software have a look at http://sunsite.icm.edu.pl/mysql/ . Is there any documentation about integrating biological information in relational databases, any staring points? that's lots of text with minimal help - however maybe we start a discussion, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | fax :+44-(0)171-269-3534 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ From owner-software@net.bio.net Wed Aug 11 00:01:00 1999 Path: biosci!bloom-beacon.mit.edu!eecs-usenet-02.mit.edu!netnews.com!howland.erols.net!newsfeed.fast.net!uunet!ffx.uu.net!news7-gui.server.ntli.net!ntli.net!not-for-mail From: Newsgroups: bionet.software Subject: Assistance required from anyone in the UK Date: 11 Aug 1999 00:46:21 GMT Organization: NTL Internet News Service Lines: 12 Message-ID: <7oqh4t$l5k$2589@nclient7-gui.server.ntli.net> NNTP-Posting-Host: p44-castor-gui.tch.cableol.net X-Trace: nclient7-gui.server.ntli.net 934332381 21684 194.168.5.44 (11 Aug 1999 00:46:21 GMT) X-Complaints-To: postmaster@ntli.net NNTP-Posting-Date: 11 Aug 1999 00:46:21 GMT Hello, people . . . Has anyone in the UK tried Totalserve free access because Ive been asked to market it and I'd never heard of it before. Its new but I would like some feedback about it as I don't want to add a naff service to my range!! Me and a few people I know have tried it and it seems either very stable and fast or completely unable to connect depending what hardware you use!!!! If there is anyone who isn't on it who wants to give it a whirl and give some feedback I'd be grateful, you can access it through my site at http://www.puk.co.uk you can hook up direct from there without a disc. You can either reply to this with feedback or email me at web@puk.co.uk Many thanks for any assistance you can provide Adrian Paris 21st Century UK Internet and Telecoms Services www.puk.co.uk web@puk.co.uk I appolagise if this is a repost, my program crashed last time . . . From owner-software@net.bio.net Wed Aug 11 08:56:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.enteract.com!newspeer.monmouth.com!nntp2.deja.com!nnrp1.deja.com!not-for-mail From: zgudmunt@my-deja.com Newsgroups: bionet.software Subject: AceDraw in physical mapping:compiling problems Date: Wed, 11 Aug 1999 09:38:18 GMT Organization: Deja.com - Share what you know. Learn what you don't. Lines: 10 Message-ID: <7orgaa$too$1@nnrp1.deja.com> NNTP-Posting-Host: 193.4.196.222 X-Article-Creation-Date: Wed Aug 11 09:38:18 1999 GMT X-Http-User-Agent: Mozilla/4.61 [en] (WinNT; I) X-Http-Proxy: 1.0 proxy.decode.is:8080 (Squid/2.1.PATCH2), 1.0 x27.deja.com:80 (Squid/1.1.22) for client 172.18.253.134, 193.4.196.222 X-MyDeja-Info: XMYDJUIDzgudmunt I have been checking out the software package named AceDraw, a program for building physical maps. A search for "acedraw" seems to generate no hits when searching the newsgroups, so I was wondering if this program was widely used..... Gudmundur Sent via Deja.com http://www.deja.com/ Share what you know. Learn what you don't. From owner-software@net.bio.net Wed Aug 11 13:07:00 1999 Path: biosci!POST.VALHALLA.NET!leo21 From: leo21@POST.VALHALLA.NET (ececool) Newsgroups: bionet.software Subject: EC Date: 11 Aug 1999 07:06:33 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 75 Sender: daemon@net.bio.net Distribution: world Message-ID: <199908111075SAA41301@mincrovsw.eng.ukm.my> NNTP-Posting-Host: net.bio.net GRAB (EC), THE NEW HOT SOFTWARE, AND FIND OUT THE MANY WAYS IT CAN MAKE YOU MONEY! TRY IT FOR F R E E TODAY! =================================================== We asked 3 major opt-in mailing companies to promote EC. All refused! The first said EC is "TOO HOT!" The second said EC is "CONTROVERSIAL!" The third said EC will "STRIP all sites NAKED!" 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