From owner-software@net.bio.net Sun Feb 01 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news-lond.gip.net!news.gsl.net!gip.net!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: ctzhang@tju.edu.cn (chun ting zhang) Newsgroups: bionet.software Subject: software to print protein structure images Date: 2 Feb 1998 16:48:47 -0000 Lines: 10 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6b4tdf$k79@mserv1.dl.ac.uk> Apparently-To: bio-soft@dl.ac.uk Dear netters: By what software (for PC) I can use to print out high quality protein images, for example, ribbons or cartoons. Thank you very much in advance. R. Zhang E-mail address: ctzhang@tju.edu.cn From owner-software@net.bio.net Sun Feb 01 22:00:00 1998 From: brais@gte.net To: brais@gte.net Subject: Corrupted Data files Date: Sun, 01 Feb 1998 23:01:43 -0600 Reply-To: braispa2@mail.northgrum.com Message-ID: <886395353.1341128719@dejanews.com> Newsgroups: bionet.software Organization: Deja News Posting Service Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!logbridge.uoregon.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Mon Feb 02 04:55:54 1998 GMT X-Authenticated-Sender: brais@gte.net X-Http-User-Agent: Mozilla/3.03Gold (Win95; I) X-Originating-IP-Addr: 153.37.99.238 (1Cust238.tnt17.lax3.da.uu.net) Lines: 10 In opening word perfect 6.1 for windows files I get a bunch of garbage characters. After attempting to recover from backup I get the error that says that the header is corrupted. What I would like to know if anyone has had any experience with retrieving information under similar circumstances. I have probably 100 files and none of them are readable. Is there a utility available which can read and repair the header information? Thanks in advance for any information or help. -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-software@net.bio.net Sun Feb 01 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news.mu-luebeck.de!not-for-mail From: "Lars Komorowski" Newsgroups: bionet.software Subject: HPLC-Manager-Software Date: Mon, 2 Feb 1998 20:49:42 +0100 Organization: Med. Universitaet zu Luebeck Lines: 6 Message-ID: <6b588e$9de$1@gwsun.medinf.mu-luebeck.de> NNTP-Posting-Host: 141.83.167.168 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Who can help me ? I lost data from HPLCManager 3.0 for DOS from Pharmacia LKB. And I don't have the disks anymore (they were from 1991). Who can send me the installation files or maybe newer ones if they work ? Lars From owner-software@net.bio.net Sun Feb 01 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!fnews.nuri.net!news.nuri.net!not-for-mail From: Tae-Young Ahn Newsgroups: bionet.software Subject: Re: software to print protein structure images Date: Tue, 03 Feb 1998 08:36:03 +0900 Organization: A-Lab, CNS, Seoul, Korea Lines: 24 Message-ID: <34D65862.50B12C7A@nuri.net> References: <6b4tdf$k79@mserv1.dl.ac.uk> NNTP-Posting-Host: ts241-179.nuri.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: chun ting zhang X-Priority: 3 (Normal) chun ting zhang wrote: > Dear netters: > > By what software (for PC) I can use to print out high quality > protein images, for example, ribbons or cartoons. > Thank you very much in advance. > > R. Zhang > > E-mail address: ctzhang@tju.edu.cn Try RasMol. You can get freeware at http://www.umass.edu/microbio/rasmol/getras.htm ====================================================== Tae-Young "We all agree that your theory is crazy. The question which divides us is whether it is crazy enough." -- Niels Bohr From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Message-ID: <34D6D8BE.BE7451B@medgen.uu.se> Date: Tue, 03 Feb 1998 09:43:42 +0100 From: Martti Tammi Organization: University of Uppsala, Dept of Genetics and Pathology, Medical Genetics Unit X-Mailer: Mozilla 4.03 [en] (X11; I; Linux 2.0.30 i686) MIME-Version: 1.0 Newsgroups: bionet.software Subject: Re: bioinformatics? References: <6b2n9v$87p$1@spk-news1.nwnexus.com> Content-Type: multipart/alternative; boundary="------------D4C075DB1F11BCBA9274B023" NNTP-Posting-Host: munin.medgen.uu.se Lines: 91 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news-peer-east.sprintlink.net!news.sprintlink.net!Sprint!fci-se!fci!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!130.238.7.13.MISMATCH!newsfeed.uu.se!munin.medgen.uu.se --------------D4C075DB1F11BCBA9274B023 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit James Yegerlehner wrote: > Hello- > Can anyone point me to a directory of bioinformatics programs of study and > their universities? > > Thanks in advance, > Jim Since you didn't specify the type of programs you are looking for I suggest you begin with the following: http://www.genet.sickkids.on.ca/bioinfo_resources/software.html other links for bioinformatics and biocomputing courses: http://www.techfak.uni-bielefeld.de/techfak/persons/chrisb/biocourse/ http://biotech.chem.indiana.edu/pages/bioinform/biprograms_us.html http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Curric/syllabi.html http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Curric/MulAli/welcome.html http://www.ebi.ac.uk/ebi_home.html http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Curric/FDSear/welcome.html http://genome.imb-jena.de/learning.html http://www.vsms.nottingham.ac.uk/vsms/index.html http://www.cs.sandia.gov/~scistra/course http://cmgm.stanford.edu/biochem218/ http://www.hgmp.mrc.ac.uk/Public/Docs/Courses/index.html http://www.cs.jhu.edu/~salzberg/cs439.html -martti tammi PhD stud bioinformatics -- Martti Tammi UPPSALA UNIVERSITY Bandstolsvaegen 20 Biomedical Center S-756 46 UPPSALA Department of Genetics and Pathology Home: +46 18 30 31 13 Unit of Medical Genetics, BOX 589 BMC: +46 18 471 4107 S-751 24 UPPSALA, Sweden Fax +46 18 52 68 49 http://www.medgen.uu.se --------------D4C075DB1F11BCBA9274B023 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit James Yegerlehner wrote:
Hello-
Can anyone point me to a directory of bioinformatics programs of study and
their universities?

Thanks in advance,
Jim

Since you didn't specify the type of programs you are looking for I suggest you begin with the following:
http://www.genet.sickkids.on.ca/bioinfo_resources/software.html

other links for bioinformatics and biocomputing courses:
http://www.techfak.uni-bielefeld.de/techfak/persons/chrisb/biocourse/
http://biotech.chem.indiana.edu/pages/bioinform/biprograms_us.html
http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Curric/syllabi.html
http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Curric/MulAli/welcome.html
http://www.ebi.ac.uk/ebi_home.html
http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Curric/FDSear/welcome.html
http://genome.imb-jena.de/learning.html
http://www.vsms.nottingham.ac.uk/vsms/index.html
http://www.cs.sandia.gov/~scistra/course
http://cmgm.stanford.edu/biochem218/
http://www.hgmp.mrc.ac.uk/Public/Docs/Courses/index.html
http://www.cs.jhu.edu/~salzberg/cs439.html

-martti tammi PhD stud
bioinformatics
  

-- 
Martti Tammi                            UPPSALA UNIVERSITY 
Bandstolsvaegen 20                      Biomedical Center
S-756 46  UPPSALA                       Department of Genetics and Pathology
Home: +46 18  30 31 13                  Unit of Medical Genetics, BOX 589
BMC:  +46 18  471 4107                  S-751 24 UPPSALA, Sweden
Fax   +46 18  52 68 49                  http://www.medgen.uu.se
  --------------D4C075DB1F11BCBA9274B023-- From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Message-ID: <34D6D993.44941FCC@medgen.uu.se> Date: Tue, 03 Feb 1998 09:47:16 +0100 From: Martti Tammi Organization: University of Uppsala, Dept of Genetics and Pathology, Medical Genetics Unit X-Mailer: Mozilla 4.03 [en] (X11; I; Linux 2.0.30 i686) MIME-Version: 1.0 Newsgroups: bionet.software Subject: Re: bioinformatics? References: <6b2n9v$87p$1@spk-news1.nwnexus.com> Content-Type: multipart/alternative; boundary="------------F1AE668CDDB14B1A112CE64F" NNTP-Posting-Host: munin.medgen.uu.se Lines: 55 Path: biosci!agate!howland.erols.net!news2.chicago.iagnet.net!131.103.1.114!news1.chicago.iagnet.net!qual.net!iagnet.net!195.74.75.15!fci-se!fci!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!130.238.7.13.MISMATCH!newsfeed.uu.se!munin.medgen.uu.se --------------F1AE668CDDB14B1A112CE64F Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit James Yegerlehner wrote: > Hello- > Can anyone point me to a directory of bioinformatics programs of study and > their universities? > > Thanks in advance, > Jim A linux site: http://www-ocean.tamu.edu/~baum/linuxlist-a.html -- Martti Tammi UPPSALA UNIVERSITY Bandstolsvaegen 20 Biomedical Center S-756 46 UPPSALA Department of Genetics and Pathology Home: +46 18 30 31 13 Unit of Medical Genetics, BOX 589 BMC: +46 18 471 4107 S-751 24 UPPSALA, Sweden Fax +46 18 52 68 49 http://www.medgen.uu.se --------------F1AE668CDDB14B1A112CE64F Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit James Yegerlehner wrote:
Hello-
Can anyone point me to a directory of bioinformatics programs of study and
their universities?

Thanks in advance,
Jim

A linux site:
http://www-ocean.tamu.edu/~baum/linuxlist-a.html
  
-- 
Martti Tammi                            UPPSALA UNIVERSITY 
Bandstolsvaegen 20                      Biomedical Center
S-756 46  UPPSALA                       Department of Genetics and Pathology
Home: +46 18  30 31 13                  Unit of Medical Genetics, BOX 589
BMC:  +46 18  471 4107                  S-751 24 UPPSALA, Sweden
Fax   +46 18  52 68 49                  http://www.medgen.uu.se
  --------------F1AE668CDDB14B1A112CE64F-- From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!agate!howland.erols.net!feed1.news.erols.com!feed2.news.erols.com!news1.best.com!nntp1.ba.best.com!shell7.ba.best.com!jquinn From: Greg Newsgroups: bionet.software Subject: Re: software to print protein structure images Date: 3 Feb 1998 04:40:12 GMT Organization: BEST Internet Communications, Inc. Lines: 15 Distribution: bionet Message-ID: <6b673c$k4g$1@nntp1.ba.best.com> References: <6b4tdf$k79@mserv1.dl.ac.uk> NNTP-Posting-Host: shell7.ba.best.com X-Trace: 886480812 20624 jquinn 206.184.139.132 X-Newsreader: TIN [UNIX 1.3 unoff BETA 970731; i386 FreeBSD 2.2.5-STABLE] chun ting zhang wrote: > Dear netters: > By what software (for PC) I can use to print out high quality > protein images, for example, ribbons or cartoons. > Thank you very much in advance. Per Kraulis has written a very good program called Molscript which is able to ouput high quality cartoons of proteins. You need to sign a license to get it, but there is (I think still) no charge. Raster3d is an excellent set of programs which output high quality images. Both Molscript and Raster3d are command line programs and have been compiled for the PC by various people. Rasmol, also available for the PC, is of course also able to output ribbon and cartoon images but the last time I checked, these were not really of publication quality (someone please correct me if I am wrong). From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!agate!howland.erols.net!EU.net!newsfeed.Austria.EU.net!Austria.EU.net!not-for-mail From: Gerald Loeffler Newsgroups: bionet.software Subject: Re: Data Analysis Date: Tue, 03 Feb 1998 13:35:12 +0100 Organization: Boehringer Ingelheim Vienna (Bender Wien) Lines: 43 Message-ID: <34D70F00.DB4@bender.co.at> References: <34CDE0B8.5A4D007C@tc.umn.edu> Reply-To: loeffler@bender.co.at NNTP-Posting-Host: apollon.bender.co.at Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.02 (WinNT; I) Hi! I'm currently in the process of getting my company to buy such a piece of software. I got the impression that S-PLUS my Mathsoft is being used by several people with success. A look at the web-page certainly looked encouraging, and so I decided to opt for S-PLUS. The strength of S-PLUS seems to be in exploratory data analysis and statistical functions. By exploratory I (or rather mathsoft!!!) mean the quick, interactive looking at various aspects of a large, multi-dimensional data-set to discover patterns. This aspect is important for me and also seems to be what Alan needs. Here in Austria, the price would be a bit less than $3000 for a Win32 version. A lot, but acceptable. cheers, gerald Alan J. Robinson wrote: > > I would like to be able to do relatively simple manipulation and > analysis of data sets, along the lines of the basic capabilities of > SAS. As you may know, statistics packages like SAS, (and ESPECIALLY > SAS) are VERY expensive. Are there other tools out there in the UNIX > and Windows95 world which will do pretty much the same thing? (I've > found spread sheets to be rather clumsy for this sort of thing.) > > (What I have in mind is doing data exploration on the output of the DSSP > program for PDB protein structures.) > > Alan J. Robinson > robin073@tc.umn.edu -- Gerald Loeffler - Bioinformaticist Boehringer Ingelheim Vienna (aka: Bender Wien) Email: loeffler@bender.co.at Phone: +43 1 80105 338 and +43 676 3289588 Fax: +43 1 8041540 Smail: Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!news-ge.switch.ch!surfnet.nl!ruu.nl!gillies From: Malcolm Gillies Newsgroups: bionet.software Subject: Re: Data Analysis Date: 3 Feb 1998 13:09:13 GMT Organization: Utrecht University, The Netherlands Lines: 41 Message-ID: <6b74tp$anq$1@news.cc.ruu.nl> References: <34CDE0B8.5A4D007C@tc.umn.edu> <34D70F00.DB4@bender.co.at> NNTP-Posting-Host: cmcind.far.ruu.nl Originator: gillies@cmcind >Alan J. Robinson wrote: >> I would like to be able to do relatively simple manipulation and >> analysis of data sets, along the lines of the basic capabilities of >> SAS. As you may know, statistics packages like SAS, (and ESPECIALLY >> SAS) are VERY expensive. Are there other tools out there in the UNIX >> and Windows95 world which will do pretty much the same thing? (I've >> found spread sheets to be rather clumsy for this sort of thing.) In article <34D70F00.DB4@bender.co.at>, Gerald Loeffler wrote: >I'm currently in the process of getting my company to buy such a piece >of software. I got the impression that S-PLUS my Mathsoft is being used >by several people with success. A look at the web-page certainly looked >encouraging, and so I decided to opt for S-PLUS. I've had some success with the "R" package, which implements a language very close to "S", as used in S-Plus (it's close enough that I managed to port an S-plus extension written in F77 from the Statlib S Archive without any problems, but I may have just been lucky). R is free under the Gnu Public License. The current release is 0.61.1, but I've found it to be reasonably complete and stable. See: The R Home Page http://www.stat.auckland.ac.nz/r/r.html R FAQ http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html cheers, Malcolm -- Malcolm Gillies PhD Student, computational medicinal chemistry Dept Medicinal Chemistry, Faculty of Pharmacy Utrecht University, The Netherlands From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!sanbi.ac.za!andrey From: andrey@sanbi.ac.za (Andrey A Ptitsyn) Newsgroups: bionet.software Subject: Re: software to print protein structure images Date: 3 Feb 1998 03:04:52 -0800 Organization: SANBI Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <34D6E985.FBB50C83@sanbi.ac.za> References: <6b4tdf$k79@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net Try WPDB from San Diego Supercomputer Center, http://www.sdsd.edu/CCMS/Packages/Wpdb.html chun ting zhang wrote: > > Dear netters: > > By what software (for PC) I can use to print out high quality > protein images, for example, ribbons or cartoons. > Thank you very much in advance. > > R. Zhang > > E-mail address: ctzhang@tju.edu.cn From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!europa.clark.net!194.159.255.21!dispose.news.demon.net!demon!news.demon.co.uk!demon!mail2news.demon.co.uk!pdchem.demon.co.uk!Paul From: Paul@pdchem.demon.co.uk (Paul Davis) Newsgroups: bionet.software Subject: Re: software to print protein structure images Date: Tue, 03 Feb 98 09:54:57 GMT Organization: Myorganisation Distribution: bionet Message-ID: <886499697snz@pdchem.demon.co.uk> References: <6b4tdf$k79@mserv1.dl.ac.uk> <6b673c$k4g$1@nntp1.ba.best.com> Reply-To: Paul@pdchem.demon.co.uk X-Mail2News-User: Paul@pdchem.demon.co.uk X-Mail2News-Path: pdchem.demon.co.uk X-Trace: mail2news.demon.co.uk 886499786 11551 Paul pdchem.demon.co.uk X-Complaints-To: abuse@demon.net X-Newsreader: Demon Internet Simple News v1.30 Lines: 23 In article <6b673c$k4g$1@nntp1.ba.best.com> jquinn@shell7.ba.best.com "Greg" writes: > > Per Kraulis has written a very good program called Molscript which is able to > ouput > high quality cartoons of proteins. You need to sign a license to get it, but > there is > (I think still) no charge. Also see the following article:- Robert M. Esnouf (1997). "An extensively modified version of MolScript that includes greatly enhanced coloring capabilities". Journal of Molecular Graphics and Modelling vol 15 p132-134. -Paul -- -------------------------------------------------------------------- Paul Davis paul@pdchem.demon.co.uk From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Sender: thomas@evolution.bmc.uu.se To: "James Yegerlehner" Newsgroups: bionet.software Subject: Re: bioinformatics? References: <6b2n9v$87p$1@spk-news1.nwnexus.com> From: Thomas Sicheritz Date: 03 Feb 1998 10:39:27 +0100 Message-ID: Lines: 27 X-Newsreader: Gnus v5.5/XEmacs 20.3 - "Vatican City" NNTP-Posting-Host: evolution.bmc.uu.se Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!195.74.75.15!fci-se!fci!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!130.238.7.13.MISMATCH!newsfeed.uu.se!evolution.bmc.uu.se "James Yegerlehner" writes: > Hello- > Can anyone point me to a directory of bioinformatics programs of study and > their universities? > > Thanks in advance, > Jim Undergraduate and graduate courses at Uppsala University http://evolution.bmc.uu.se/~siv/gnomics/courses.html Courses at George Mason University http://www.science.gmu.edu/~michaels/Bioinformatics/#p1 -thomas -- Sicheritz Ponten Thomas E. Department of Molecular Biology Biomedical Center Uppsala University BMC: +46 18 4714214 BOX 590 S-751 24 UPPSALA Sweden Fax +46 18 557723 http://evolution.bmc.uu.se/~thomas Molecular Tcl: http://evolution.bmc.uu.se/~thomas/tcl Molecular Linux: http://evolution.bmc.uu.se/~thomas/mol_linux De Chelonian Mobile ... The Turtle Moves ... From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!newsfeed.internetmci.com!199.0.154.56!ais.net!ix.netcom.com!news From: "Joseph James" Newsgroups: bionet.software Subject: Software Engineering Date: Tue, 3 Feb 1998 16:12:29 -0500 Organization: Netcom Lines: 30 Message-ID: <6b815q$2ts@dfw-ixnews12.ix.netcom.com> NNTP-Posting-Host: nwk-nj13-10.ix.netcom.com X-NETCOM-Date: Tue Feb 03 3:11:22 PM CST 1998 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 I am a semi-retired software engineer and technical writer with thirty years of professional experience, most of it acquired through the development of complex applications for scientists and mathematicians involved in research, as well as for Fortune 500 corporations in the United States. During the last decade, I've created custom software for an international clientele as an internet-based developer. I specialize in the rapid, cost-effective prototyping of scientific and mathematical applications (for both small-circle research use and for commercial deployment), and I only work on one project at a time. I do not have a website and do no advertising other than occasional newsgroup messages like this one. If you have a serious interest in developing a prototype of a software system which meets the abovementioned criteria, please feel free to contact me by email using the address below for a free consultation, without any cost or obligation whatsoever. If your application interests me sufficiently, I will prototype it free of charge in exchange for your willingness to provide an honest business reference and appraisal of my work to other potential clients, upon request. Joseph James qtechsofXXX-AT-XXXix.netcom.com (SPAM GUARD: replace the characters "XXX-AT-XXX" with the character "@" to obtain my actual email address.) From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!news.maxwell.syr.edu!news.cis.ohio-state.edu!magnus.acs.ohio-state.edu!rrumpf From: rrumpf@postbox.acs.ohio-state.edu (Dr. Robert Rumpf) Newsgroups: bionet.software Subject: Alpha Innotech ProScan RFLP software - Opinions? Date: Tue, 03 Feb 1998 13:44:46 -0500 Organization: The Ohio State University Dept. of Oral Biology Lines: 14 Message-ID: NNTP-Posting-Host: 128.146.74.139 X-Newsreader: MT-NewsWatcher 2.3.5 We're looking for some good software that will analyze band patterns from multiple reactions and establish a profile database which can then be searched for pattern matches. We've seen literature on the Alpha Innotech ProScan stuff and were wondering what the net opinion was. Is there anything better out there? We can use PC or Mac but prefer Mac by far... ************************************************************************ * Dr. Robert Rumpf - rumpf.1@osu.edu - http://www.marcon.org/users/bob * * * * It is by caffeine alone that I set my mind in motion * * By the beans of java, my thoughts acquire speed * * The hands acquire the shakes, the shakes become a warning * * It is by caffeine alone that I set my mind in motion * ************************************************************************ From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!xfer.kren.nm.kr!news.maxwell.syr.edu!news-ge.switch.ch!news.grnet.gr!news.ntua.gr!not-for-mail From: "George Liakopoulos" Newsgroups: bionet.software Subject: Re: software to print protein structure images Date: Tue, 3 Feb 1998 20:32:39 +0200 Organization: Lab of Plant Physiology Lines: 16 Message-ID: <6b7o0c$pma$1@ulysses.noc.ntua.gr> References: <6b4tdf$k79@mserv1.dl.ac.uk> NNTP-Posting-Host: pe3pc41.aua.ariadne-t.gr X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Hi, Try the WEBLAB VIEWER. ITS GOOD!!! The address: http://www.msi.com/weblab/viewer Then, you have to provide the program with protein sequencies. Try the following for start: http://expasy.hcuge.ch/ I hope this helps. George Liakopoulos Post graduate student Lab of Plant Physiology Agricultural University of Athens HELLAS email: karab@auadec.aua.ariadne-t.gr From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!agate!howland.erols.net!EU.net!news0.Belgium.EU.net!newsr.Belgium.EU.net!not-for-mail From: "Gaëtan MERCENIER" Newsgroups: bionet.software Subject: Hosting for Softwares... Date: Tue, 3 Feb 1998 17:04:36 +0100 Organization: EUnet Belgium, Leuven, Belgium Lines: 8 Message-ID: <6b7b8h$d70$1@news3.Belgium.EU.net> NNTP-Posting-Host: dialup129.liege.eunet.be X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Hello ! I can host your softwares at competitive rates. If you are interested: webmaster@gate2net.com . (Including sub-domains or domain names) From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.mindspring.net!cssun.mathcs.emory.edu!cronkite.cc.uga.edu!twopaths From: russell@dogwood.botany.uga.edu (Russell Malmberg) Newsgroups: bionet.software Subject: announce Peaks software to analyze HPLC data Date: Tue, 03 Feb 1998 13:34:33 GMT Organization: Botany Department, University of Georgia Lines: 60 Message-ID: <6b76b2$s0e$1@cronkite.cc.uga.edu> NNTP-Posting-Host: twopaths.botany.uga.edu Keywords: software, HPLC, integrate, Windows NT X-Newsreader: News Xpress 2.01 Peaks Software availability: http://www.botany.uga.edu/malmberg/software.html Peaks is a utility to analyze data from an HPLC or similar instrument. Peaks was written to analyze data from our laboratory HPLC which consisted of a time axis, and a y-axis, where we wished to integrate areas under the various peaks in our data. This data typically comes from laboratory instruments that are connected by an Analog to Digital card to a computer. The current version of Peaks is fully windowed, and includes both text and graphical output. Peaks is a 32 bit program for Windows NT or Windows 95. Versions are available for Intel and for DEC alpha processors. A major advantage of Peaks is that it is free. This is the product of my first serious C++ programming exercise. I wrote it to learn C++ and windows programming, and because my laboratory colleagues needed such a program. Peaks fills a need we had, and I’m distributing it in the hopes it is useful to others. It probably has bugs and various unanticipated methods of crashing (use at your own risk), but it seems to work. Please send me an e-mail if you find it useful, or when you find a bug. A few other biology programs for Windows NT are available at my web site. These are typically programs that someone else wrote, and they were gracious enough to allow me to compile them for windows NT. These include: ClustalW for a DEC Alpha. ClustalX for a DEC Alpha. GeneDoc 2.2 for a DEC Alpha. MapMaker and QTL for a DEC Alpha. Molphy 2.2 (Protml) for a DEC Alpha. NCBI programs Nentrez, Blast client, Sequin for a DEC Alpha. Peaks 0.8 for a DEC Alpha. Phylip 3.57 for a DEC Alpha. ReadSeq for a DEC Alpha. SeqPup 0.5 for a DEC Alpha. ----------------------------- MapMaker and QTL for an Intel. Molphy 2.2 (Protml) for an Intel. Peaks 0.8 for an Intel. Note that DEC alpha binaries will not run on an Intel CPU computer. Russell L. Malmberg Botany Department University of Georgia Athens, GA 30602-7271 e-mail. russell@dogwood.botany.uga.edu web page. http://www.botany.uga.edu/malmberg/ ----- Russell L. Malmberg russell@dogwood.botany.uga.edu http://dogwood.botany.uga.edu/malmberg/ From owner-software@net.bio.net Mon Feb 02 22:00:00 1998 Date: Tue, 03 Feb 1998 12:34:29 +0100 From: zjons@vetbio.unizh.ch (Zophonias O. Jonsson) Newsgroups: bionet.software Distribution: bionet Subject: Re: software to print protein structure images Message-ID: References: <6b4tdf$k79@mserv1.dl.ac.uk> Organization: Universitat Zurich-Irchel NNTP-Posting-Host: 130.60.120.27 Lines: 36 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!news-zh.switch.ch!rzunews1.unizh.ch!NewsWatcher!user In article <6b4tdf$k79@mserv1.dl.ac.uk>, ctzhang@tju.edu.cn (chun ting zhang) wrote: > Dear netters: > > By what software (for PC) I can use to print out high quality > protein images, for example, ribbons or cartoons. > Thank you very much in advance. > > R. Zhang > > E-mail address: ctzhang@tju.edu.cn My personal favourit is the Swiss-PdbViewer available freely at http://www.expasy.ch/spdbv/mainpage.htm I have tried both the Mac and PC versions (2.6) and both of them do a very decent job (either on a Power Mac 8600/200 or a P166 PC). You will need the QuickDraw3D library from apple to run the program, but that is available for free, and if you want to generate really nice ray traced images you can export the scenes that you generate to POV-ray (a freeware rendering program). My compliments to Nicolas Guex and Manuel C. Peitsch for an excellent program! Zophonias _____________________________________________________________________ Zophonias O. Jonsson Institut fur Veterinarbiochemie Tel: (41-1)-635-54-75 Universitat Zurich-Irchel Fax: (41-1)-635-68-16 Winterthurerstrasse 190 CH-8057 Zurich Switzerland _____________________________________________________________________ From owner-software@net.bio.net Tue Feb 03 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!204.71.76.137!news.campus.mci.net!n-f-m From: "Michael W. Thompson" Newsgroups: bionet.software Subject: Re: Corrupted Data files Date: Wed, 04 Feb 1998 16:07:09 -0500 Organization: CampusMCI Lines: 29 Message-ID: <34D8D87D.5F96FD46@nospam.noway.nohow> References: <886395353.1341128719@dejanews.com> Reply-To: nospam@nospam.noway.nohow NNTP-Posting-Host: s18-pm05.uky.campus.mci.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.02 [en] (Win95; I) brais@gte.net wrote: > In opening word perfect 6.1 for windows files I get a bunch of garbage > characters. After attempting to recover from backup I get the error that > says that the header is corrupted. What I would like to know if anyone > has had any experience with retrieving information under similar > circumstances. I have probably 100 files and none of them are readable. > Is there a utility available which can read and repair the header > information? Thanks in advance for any information or help. Sounds like you might have a word "macro virus"-- we had one on our lab computer that caused some similar symptoms. An up-to-date virus checker (you can find those at download.com or any similar site) will take care of the problem, if that is indeed the problem. Hope that helps. replies-- post here. I refuse to post my real email address here due to the deluge of SPAM that it causes. -- Michael W. Thompson Univ. of Kentucky, Dept. of Biochemistry Western Kentucky Photo Gallery: http://sac.uky.edu/~mthom0/sitemap.htm Wildflowers of Western Kentucky: http://sac.uky.edu/~mthom0/flora.htm From owner-software@net.bio.net Tue Feb 03 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!ais.net!vixen.cso.uiuc.edu!news.indiana.edu!news.iupui.edu!not-for-mail From: "Charlie Mantel" Newsgroups: bionet.software Subject: Re: Dot blot analyzer Date: Tue, 3 Feb 1998 23:28:55 -0500 Organization: Indiana University - Purdue Univeristy At Indianapols,IN Lines: 11 Message-ID: <6b8rug$mrp$1@hercules.iupui.edu> References: <34D1FCB5.768A@ipst.edu> NNTP-Posting-Host: c1p38.dialin.iupui.edu X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Try these links:: http://facs.scripps.edu/ http://facs.scripps.edu/software.html I use the program, WinMDI, and I swear by it. You can do almost any kind of regional analysis with stats in color, histograms, density plots, etc. They are all copyable and you can paste them directly into popular presentation programs like freelance or powerpoint. You can download several versions of the program from these sites. Good luck. From owner-software@net.bio.net Tue Feb 03 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!newsfeed.internetmci.com!152.163.199.19!portc03.blue.aol.com!audrey02.news.aol.com!not-for-mail From: zevsolltec@aol.com (ZevSolltec) Newsgroups: bionet.software Subject: Re: Alpha Innotech ProScan RFLP software - Opinions? Date: 4 Feb 1998 15:16:03 GMT Lines: 17 Message-ID: <19980204151601.KAA28513@ladder02.news.aol.com> NNTP-Posting-Host: ladder02.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com References: Dear Dr. Rumpf, If you prefer Mac software, see our website or contact me for more information. Best regards, Zev --------------------------------------------------------------------------- Zev Sunleaf Vice President Solltech, Inc. Technology Innovation Center Oakdale, IA 52319 (319) 335-4702 (319) 335-4489 Fax Email: ZevSolltec@aol.com http://members.aol.com/ZevSolltec/DENDRON.html --------------------------------------------------------------------------- From owner-software@net.bio.net Tue Feb 03 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.gip.net!news.gsl.net!gip.net!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!feed1.news.luth.se!luth.se!news.algonet.se!newsfeed1.telenordia.se!newsfeed1.funet.fi!news.funet.fi!news.helsinki.fi!not-for-mail From: Dag Stenberg Newsgroups: bionet.software Subject: Spectral analysis of EEG Date: 4 Feb 1998 07:29:00 GMT Organization: University of Helsinki Lines: 21 Message-ID: <6b95bs$h88$1@oravannahka.Helsinki.FI> NNTP-Posting-Host: vesuri.helsinki.fi X-Newsreader: TIN [UNIX 1.3 unoff BETA 970613; alpha OSF1 V4.0] A colleague asked the following: - he has sampled EEG data and feels able to convert this into any other digital format - he wants to do FFTs and postprocessing of spectral parameters, but does not want to buy a complete sampling-analysis package (like Spike2, Datawave, CVMS etc.), because of the cost - What ready-made software could he get, so he does not have to find somebody to write spectral analysis programs for the umpteenth time in history? Dag Stenberg Spike2 and Datawave user ------------------------------------------------------------------ Dag Stenberg MD PhD stenberg@cc.helsinki.fi Institute of Biomedicine tel: (int.+)358-9-1918532 Department of Physiology fax: (int.+)358-9-1918681 P.O.Box 9 (Siltavuorenpenger 20 J) FIN-00014 University of Helsinki,Finland ------------------------------------------------------------------ From owner-software@net.bio.net Tue Feb 03 22:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!uninett.no!sn.no!nntp.uio.no!funny.bahnhof.se!not-for-mail From: Per Kraulis Newsgroups: bionet.software Subject: Re: software to print protein structure images Date: Wed, 04 Feb 1998 19:01:57 +0100 Organization: Avatar Software AB Lines: 19 Message-ID: <34D8AD15.794B@avatar.se> References: <6b4tdf$k79@mserv1.dl.ac.uk> <6b7o0c$pma$1@ulysses.noc.ntua.gr> NNTP-Posting-Host: pm2-30.bahnhof.se Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) chun ting zhang wrote: > By what software (for PC) I can use to print out high quality > protein images, for example, ribbons or cartoons. You could try MolScript v2.0 which produces PostScript, VRML 2.0 and Raster3D files from an input script and a PDB file. There is also an OpenGL interactive graphics mode, and JPEG, PNG ad EPS image file output formats, but these require additional libraries. The program is written in C (ANSI), and reportedly compiles with GNU's gcc. For more information, see the Official MolScript Web Site at http://www.avatar.se/molscript/ where the documentation, license conditions (free for academics and students) and distribution instructions can be found /Per Kraulis From owner-software@net.bio.net Wed Feb 04 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.direct.ca!news-peer.sprintlink.net!news-peer-east.sprintlink.net!news.sprintlink.net!Sprint!rill.news.pipex.net!pipex!main.de.uu.net!Ireland.EU.net!HEAnet!web3.tcd.ie!acer.gen.tcd.ie!tpwalsh From: tpwalsh@acer.gen.tcd.ie (Tom Walsh) Newsgroups: bionet.software Subject: Re: PDB amino acid positions Date: 5 Feb 1998 14:07:28 GMT Organization: INCBI Lines: 28 Message-ID: <6bch30$lqo@web3.tcd.ie> References: <34D98C11.41C6@cc.huji.ac.il> NNTP-Posting-Host: acer.gen.tcd.ie In article <34D98C11.41C6@cc.huji.ac.il>, Iddo Friedberg wrote: >Hi All, > >Does anybody know of a good, robust program which will accept a PDB >file as input, and for the output deliver for each amino acid it's PDB >position number. Including such vagaries as negative numbering (some >files have them), and non-numerical positions (as in serine proteinases, >where there are such things as 65A). > If I've understood the problem correctly, it should be trivial in AWK. Tom Walsh >Please reply by email, as well as to this newsgroup. > > >Many thanks, > >Iddo > -- - You talk to me of nationality, language, religion. I shall try to fly by those nets. From owner-software@net.bio.net Wed Feb 04 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!woodstock.news.demon.net!demon!bullseye.news.demon.net!demon!mega.demon.nl!not-for-mail From: "Mellow Yellow" Newsgroups: bionet.software Subject: LQQKING FOR NEW SOFTWARE LIST?? Date: Thu, 5 Feb 1998 06:30:58 +0100 Message-ID: <886656676.8992.0.rover.c3adec73@news.demon.nl> NNTP-Posting-Host: mega.demon.nl X-NNTP-Posting-Host: mega.demon.nl [195.173.236.115] X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Lines: 26 Zijn jullie op zoek naar de nieuwste software en games cd's??? Dan zijn jullie aan het goede adres. wij leveren o.a : Crazy Bites Legacy Twilight Holland With love Mega Pack en nog veel meer meer meer. Wij zijn misschien niet de goedkoopste maar wel de beste.!!!! Voor vragen of suggesties kunt mailen naar postbus@mega.demon.nl Wilt U kijken op onze site dat kan ook http:\\www.tmyt.demon.nl Verder wensen wij U veel plezier en hopen dat wij wat voor U kunnen doen. Met vriendelijke groet: Mellow & Yellow. From owner-software@net.bio.net Wed Feb 04 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!194.125.2.233!iol!stns.news.pipex.net!hose.news.pipex.net!pipex!grot.news.pipex.net!pipex!join.news.pipex.net!pipex!duke.telepac.pt!news.telepac.pt!not-for-mail From: "Luis Santos" Newsgroups: bionet.software Subject: First Sense Date: Thu, 5 Feb 1998 13:40:41 -0000 Lines: 5 Message-ID: <6bcfku$tl1$1@duke.telepac.pt> NNTP-Posting-Host: 194.65.91.87 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Anyone can tell me where to buy it. Thanks. From owner-software@net.bio.net Wed Feb 04 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!feeder.qis.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!not-for-mail From: islam Newsgroups: bionet.software Subject: Re: PDB amino acid positions Date: Thu, 05 Feb 1998 14:12:33 +0000 Organization: Imperial Cancer Research Fund Lines: 32 Message-ID: <34D9C8D1.167E@icrf.icnet.uk> References: <34D98C11.41C6@cc.huji.ac.il> NNTP-Posting-Host: palm.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX 6.3 IP32) Iddo, This is a straight forward request, but for which platforms do you need the program and how do you want the output format ? One word of caution - there may be missing residues in the data in which case the numbering may not truly represent the numberical order of the residues. Iddo Friedberg wrote: > > Hi All, > > Does anybody know of a good, robust program which will accept a PDB > file as input, and for the output deliver for each amino acid it's PDB > position number. Including such vagaries as negative numbering (some > files have them), and non-numerical positions (as in serine proteinases, > where there are such things as 65A). > > Please reply by email, as well as to this newsgroup. > > Many thanks, > > Iddo ____________________________________________ Suhail A Islam Biomolecular Modelling Laboratory Imperial Cancer Research Fund, P.O. Box 123 44 Lincoln's Inn Fields, London WC2A 3PX Tel: (0171) 269 3380, Fax: (0171) 269 3258 email: islam@icrf.icnet.uk http://www.icnet.uk/bmm/ ____________________________________________ From owner-software@net.bio.net Wed Feb 04 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!134.222.90.2!EU.net!sun4nl!star.cs.vu.nl!bio.vu.nl!usenet From: renej@bio.vu.nl Newsgroups: bionet.software Subject: Re: Spectral analysis of EEG Date: Thu, 05 Feb 1998 10:08:43 +0100 Organization: VU Biology, Amsterdam, The Netherlands Lines: 20 Message-ID: <34D9819B.A3C@bio.vu.nl> References: <6b95bs$h88$1@oravannahka.Helsinki.FI> NNTP-Posting-Host: 130.37.80.7 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.04Gold (WinNT; I) Dag Stenberg wrote: > > A colleague asked the following: > - he has sampled EEG data and feels able to convert this into any other > digital format > - he wants to do FFTs and postprocessing of spectral parameters, but > does not want to buy a complete sampling-analysis package (like Spike2, > Datawave, CVMS etc.), because of the cost > - What ready-made software could he get, so he does not have to find > somebody to write spectral analysis programs for the umpteenth time > in history? > Try the package SANTIS at: http://www.physiology.rwth-aachen.de/santis/ Hope this helps RJ From owner-software@net.bio.net Wed Feb 04 22:00:00 1998 Path: biosci!NCBI.NLM.NIH.GOV!francis From: francis@NCBI.NLM.NIH.GOV Newsgroups: bionet.software Subject: Re: Web translation utility Date: 5 Feb 1998 06:55:36 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802051454.JAA12430@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net > From BIOSCI-REQUEST@net.bio.net Thu Feb 5 09:42:05 1998 > Could someone point me to a web translation utility? I simply want to input a > DNA sequence and (after defining the reading frame), get back the peptide > sequence. Does NCBI have a utility like this? > > Answer by email, please sjhogart@unity.ncsu.edu yes, we do: from our home page you can get to the orf-finder: http://www.ncbi.nlm.nih.gov/gorf/gorf.html cheers, f. -- | B.F. Francis Ouellette | GenBank Coordinator | | francis@ncbi.nlm.nih.gov > -- > Susan > "Suicide is the most sincere form of self-criticism." - Anon > http://www4.ncsu.edu/unity/users/s/sjhogart/public/home.html > > From owner-software@net.bio.net Wed Feb 04 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!206.229.87.25!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!199.125.85.9!news.mv.net!newspump.wustl.edu!newsreader.wustl.edu!not-for-mail From: reece@whoville.wustl.edu Newsgroups: bionet.software Subject: Re: PDB amino acid positions Date: 05 Feb 1998 17:48:34 -0600 Organization: Biophysics & Biochemistry, Washington University, St. Louis, USA Lines: 40 Message-ID: <82afc5r4tp.fsf@whoville.wustl.edu> References: <34D98C11.41C6@cc.huji.ac.il> Reply-To: Reece Kimball Hart NNTP-Posting-Host: whoville.wustl.edu To: Iddo Friedberg X-Attribution: Reece X-URL: X-Newsreader: Gnus v5.5/Emacs 20.2 -----BEGIN PGP SIGNED MESSAGE----- >>>>> IF == Iddo Friedberg wrote >>>>> In bionet.software >>>>> On Thu, 05 Feb 1998 11:53:21 +0200 >>>>> Re PDB amino acid positions IF> Does anybody know of a good, robust program which will accept a PDB IF> file as input, and for the output deliver for each amino acid it's PDB IF> position number. If I understand correctly, you want the ordinal position of each amino acid. perl -ne 'if (/ATOM.{13}(...)...(....)/ and not $seen{$2}++) \ {printf("%3d $1\n",++$o)}' file.pdb (don't type the '\') The above worked on a test with perl 5.004_03 (type perl -v), 1hvr (2 chains) and 3ptb (discontinuous numbering). Whether it's 'good' or 'robust' depends on your needs, but I hope this helps. perl is freely available from www.perl.com. - -- Reece Hart, http://dasher.wustl.edu/~reece/ Do not send unsolicited bulk email. Boycott companies which do so. -----BEGIN PGP SIGNATURE----- Version: 2.6.3ia Charset: noconv Comment: Processed by Mailcrypt 3.4, an Emacs/PGP interface iQCVAwUBNNpPkkxUVHHReKr5AQEJWwP+MThx/EZnaQyHceL8PNkL/EeZ2xyKD64n FDpDbbimYq8AciDcLbdN+IM+ixtKhuK4IEsmLIuRiEBUUORtb/qQiwRT5GpN2zX8 qSgibTTpXEi4SNbSvAO0oHkKKg70cldJ+jTRgxQWgYuELS0vkmJreFO//bNYG8xX AyIb9AMAqOE= =01Os -----END PGP SIGNATURE----- From owner-software@net.bio.net Wed Feb 04 22:00:00 1998 Newsgroups: bionet.xtallography,bionet.software Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!newscore.univie.ac.at!newsfeed.ecrc.net!207.41.200.131.MISMATCH!news-pen-1.sprintlink.net!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!209.95.128.196!news-nyc.telia.net!masternews.telia.net!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!130.237.207.77.MISMATCH!news.ki.se!news From: Guoguang Lu Subject: Improve version of the TOP software package for protein structure comparisons Sender: news@news.ki.se (News admin) Message-ID: <34DA08DE.4899@alfa.mbb.ki.se> Date: Thu, 5 Feb 1998 18:45:50 GMT Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii NNTP-Posting-Host: tau.mbb.ki.se Mime-Version: 1.0 X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) Organization: Karolinska Institutet Lines: 37 Xref: biosci bionet.xtallography:4037 bionet.software:20429 Improve version of the TOP software package for automatic comparison of 3-d protein structures The TOP program for automatic comparisons of protein structures has been recently improved. The new version for unix computers can be obtained via FTP. The new version of Web server has been also installed. Please see http://gamma.mbb.ki.se/~guoguang/webtop/wwwtop.html The most significant improvement is in seraching similar structures in database. The users of old version complained about the program outputs too much infomration (noise) which is diffult to get the point. The new version gives parameters of "Structure Diveristy" and "Topological Diversity" which rank the similarity between homologous structures. It is much easier for users to find the their most similar structures in the search and igored the noise. The new version is able to find sequence permutations in the comparisons This will help to find homologous structures which is missed the other software with similar functions. Some part of the document mightbe still confusing. I need feed back from users to fix it. It is also welcome to complain about any problems of Web server and unix computers. -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Guoguang Lu, PhD, Research Scientist Division of Molecular Structural Biology Department of Medical Biochemistry and Biophysics Doktorsringen 9A1 Karolinska Institute 17177 Stockholm Sweden --------------------------------------------------------------------- Phone: (int+46)-8-728 7651(o) Email: guoguang@alfa.mbb.ki.se Fax: (int+46)-8-327626 Homepage: http://gamma.mbb.ki.se/~guoguang +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-software@net.bio.net Wed Feb 04 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!europa.clark.net!208.134.241.18!newsfeed.internetmci.com!206.252.192.28!news.stealth.net!news.ibm.net.il!ibm.net!news.biu.ac.il!news.huji.ac.il!not-for-mail From: Iddo Friedberg Newsgroups: bionet.software Subject: PDB amino acid positions Date: Thu, 05 Feb 1998 11:53:21 +0200 Organization: The Hebrew University, Jerusalem Lines: 21 Message-ID: <34D98C11.41C6@cc.huji.ac.il> NNTP-Posting-Host: bishop.md.huji.ac.il Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.2 IP22) Hi All, Does anybody know of a good, robust program which will accept a PDB file as input, and for the output deliver for each amino acid it's PDB position number. Including such vagaries as negative numbering (some files have them), and non-numerical positions (as in serine proteinases, where there are such things as 65A). Please reply by email, as well as to this newsgroup. Many thanks, Iddo -- Iddo Friedberg Phone: (972)-2-6758647 email: idoerg@cc.huji.ac.il web: http://www.ls.huji.ac.il/~idoerg More info: finger idoerg@cc.huji.ac.il From owner-software@net.bio.net Wed Feb 04 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!not-for-mail From: pd213@cam.ac.uk (Phil Davey) Newsgroups: bionet.software Subject: Re: Web translation utility Date: 5 Feb 1998 16:50:14 GMT Organization: University of Cambridge, England Lines: 26 Sender: pd@napc8.path.cam.ac.uk Message-ID: <6bcqk6$569$1@lyra.csx.cam.ac.uk> References: <199802051454.JAA12430@borduas.nlm.nih.gov> Reply-To: pd213@cam.ac.uk NNTP-Posting-Host: napc8.path.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 0.9.8 In article <199802051454.JAA12430@borduas.nlm.nih.gov>, francis@NCBI.NLM.NIH.GOV writes: >> From BIOSCI-REQUEST@net.bio.net Thu Feb 5 09:42:05 1998 >> Could someone point me to a web translation utility? I simply want to >> input a DNA sequence and (after defining the reading frame), get back >> the peptide sequence. Does NCBI have a utility like this? > > yes, we do: > > from our home page you can get to the orf-finder: > > http://www.ncbi.nlm.nih.gov/gorf/gorf.html You could also try a program I have written. It's called Sequence Tool and is at http://www.path.cam.ac.uk/~pd/tool_multi.html A slightly modified version which will process lots of sequences at once (as long as they are in fasta format) is at http://www.path.cam.ac.uk/~pd/tool_test.html At the moment it will optionally reformat, reverse complement, translate (in any frame) and print a simple base composition. Let me know what you think if you decide to try it out. -- Phil [E-mail pd213@cam.ac.uk] From owner-software@net.bio.net Wed Feb 04 22:00:00 1998 Newsgroups: bionet.software Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!uni-erlangen.de!news-nue1.dfn.de!news-lei1.dfn.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.uni-bielefeld.de!techfak.uni-bielefeld.de!fuellen From: fuellen@PLEASE_REMOVE_THIS_SPAM_BLOCKER.techfak.uni-bielefeld.de (Georg Fuellen) Subject: Re: bioinformatics? Message-ID: Sender: fuellen@TechFak.Uni-Bielefeld.DE (Georg Fuellen) Cc: fuellen Date: Thu, 5 Feb 1998 19:09:33 GMT To: "James Yegerlehner" Reply-To: fuellen References: <6b2n9v$87p$1@spk-news1.nwnexus.com> NNTP-Posting-Host: schilf.techfak.uni-bielefeld.de Organization: Universitaet Bielefeld, Technische Fakultaet. X-Newsreader: xrn 8.01 Lines: 22 In article <6b2n9v$87p$1@spk-news1.nwnexus.com>, "James Yegerlehner" writes: |> Hello- |> Can anyone point me to a directory of bioinformatics programs of study and |> their universities? Take a look at http://www.iscb.org/training.html A collection of course syllabi is also available via http://www.techfak.uni-bielefeld.de/bcd/Curric/syllabi.html Any comments, additions, corrections, etc would be welcome ! best wishes, Georg Fuellen Univ. Bielefeld, Research Group in Practical Comp. Science http://www.techfak.uni-bielefeld.de/bcd/welcome.html |> Thanks in advance, |> Jim |> |> |> From owner-software@net.bio.net Thu Feb 05 22:00:00 1998 Path: biosci!agate!howland.erols.net!europa.clark.net!152.158.16.55!newsfeed2.uk.ibm.net!ibm.net!newsgate.cistron.nl!het.net!news.worldonline.nl!not-for-mail From: "joris" Newsgroups: bionet.software Subject: PC as answeringmachine? Date: 6 Feb 1998 15:15:31 GMT Organization: World Online Lines: 8 Message-ID: <01bd330c$67d0c040$LocalHost@aplusr> NNTP-Posting-Host: dlft1-p182.worldonline.nl X-Newsreader: Microsoft Internet News 4.70.1157 Does anyone know of software available which can make a pc and modem work as an answeringmachine, including soundrecording (for instance in *.wav files)? I would be very grateful for an answer and/or a tip. Thanks a lot, Joris. From owner-software@net.bio.net Thu Feb 05 22:00:00 1998 Path: biosci!agate!ihnp4.ucsd.edu!sdd.hp.com!usc!howland.erols.net!woodstock.news.demon.net!demon!dispose.news.demon.net!demon!peer.news.zetnet.net!zetnet.co.uk!user-10002114.zetnet.co.uk!not-for-mail From: JGW Computing Newsgroups: bionet.software Subject: Re: Sample organiser software Date: Fri, 6 Feb 1998 13:53:47 GMT Message-ID: <1998020613534771355@zetnet.co.uk> References: <1998012511425771355@zetnet.co.uk> NNTP-Posting-Host: user-10002114.zetnet.co.uk X-Mailer: ZIMACS Version 1.20c 10002114 Lines: 34 The message <1998012511425771355@zetnet.co.uk> from JGW Computing contains these words: > Have you wasted lots of time looking for a blood sample you knew you > had received? Or spent ages sorting samples into order, so that you > can find them later? > Then Finder! is for you. > All you do is place your sample into a rack, then enter the sample > number into Finder! When you want to find the sample again, ask > Finder!, and it will tell you where it's stored. Brilliant, but simple. > Visit http://www.users.zetnet.co.uk/jgw.computing/ to download a > function limited working program, including a quick start guide. > Contact JGW Computing by email to: > jgw.computing@zetnet.co.uk Later version now available on the web site. Changes include: * sample numbers can contain characters, digits and decimal points * range checks on all the above * length of sample number increased to 12 characters per number * more comprehensive bar-code entry setup * limited testing of bar-code entry with new bar-code reader configuration option From owner-software@net.bio.net Fri Feb 06 22:00:00 1998 Date: Sat, 07 Feb 1998 01:30:14 +0100 From: gerard@xray.bmc.uu.se (Gerard Kleywegt) Newsgroups: bionet.software Subject: Re: PDB amino acid positions Message-ID: References: <34D98C11.41C6@cc.huji.ac.il> Organization: SBNet - Uppsala University X-Newsreader: Value-Added NewsWatcher 2.1d3+ NNTP-Posting-Host: nostromo.bmc.uu.se Lines: 25 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!194.162.162.196!newsfeed.nacamar.de!uninett.no!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!130.238.7.13.MISMATCH!newsfeed.uu.se!nostromo.bmc.uu.se!user In article <34D98C11.41C6@cc.huji.ac.il>, Iddo Friedberg wrote: >Hi All, > >Does anybody know of a good, robust program which will accept a PDB >file as input, and for the output deliver for each amino acid it's PDB >position number. Including such vagaries as negative numbering (some >files have them), and non-numerical positions (as in serine proteinases, >where there are such things as 65A). > >Please reply by email, as well as to this newsgroup. > > >Many thanks, > >Iddo cat filename.pdb | grep ^ATOM | grep CA | cut -c18-27 --cd ---------------------------------------------------------- Gerard Kleywegt mailto:gerard@xray.bmc.uu.se http://alpha2.bmc.uu.se/~gerard/ From owner-software@net.bio.net Fri Feb 06 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news-pen-15.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!news.sprintlink.net!Sprint!24.129.0.46!newsfeed.se.mediaone.net!baker.se.mediaone.net!news@ccse.net From: "Jack_D" Newsgroups: bionet.software Subject: NetConnect Date: Sat, 7 Feb 1998 06:15:02 -0000 Organization: MediaOne Express Lines: 19 Message-ID: <6bhfug$2q67@baker.se.mediaone.net> NNTP-Posting-Host: 24.129.28.74 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Beware of a company known as NetConnect, Inc. doing business out of Markham, Ontario. This company was once known as Markham Computer Corporation. They had offices in Boca Raton, FL. and are marketing a product known as NetSupport Manager. This company skipped out of the United States in the middle of the night, leaving employees and vendors holding the bag. Even personal property was taken to Canada against the owner’s wishes, and has yet to be returned. The owners of this company, the Batra’s, also run a company call Batra International. DON’T DO BUSINESS WITH THESE PEOPLE, they cannot be trusted. Court records show that they’ve skipped out of the U.S. to avoid paying outstanding bills. Try collecting something from someone in a foreign country. Senator Bob Graham of Florida is pursuing this case with the United States Justice Department. Again, be very wary about doing any kind of business with these people. Please pass this along to each agency that you think might have a need to know. From owner-software@net.bio.net Fri Feb 06 22:00:00 1998 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.software Subject: Recomb98: student financial support Date: 6 Feb 1998 16:16:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802070014.QAA08372@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net Thanks to the generosity of our governmental and corporate sponsors, limited financial support for travel expenses will be available for students attending RECOMB 98. Support is offered on a competitive basis. In order to apply for financial support, you must: 1) be a graduate student or undergraduate student attending RECOMB 98, 2) register for RECOMB 98 including the submission of registration fees by Feb. 20, 1998, 3) submit a one page essay describing why you should receive financial support. The essay (up to *500* words) should include the following information: i) your name, ii) your email address, iii) the school you are attending, iv) the professor who is overseeing your research, v) a short description of your research, vi) the paper title if you have a paper at RECOMB 98, v) a short description of your research, vi) the paper title if you have a paper at RECOMB 98, vii) the poster title if you have a poster at RECOMB 98, viii) any other information that you think would be relevant. The essay should be sent via email to support@ecology.biomath.mssm.edu by Feb. 20, 1998. Those students selected for financial support will be notified by email on or before March 9, 1998. Early registration ends February 20, 1998! Hotel conference rate ends February 24, 1998! From owner-software@net.bio.net Fri Feb 06 22:00:00 1998 Path: biosci!agate!howland.erols.net!sunqbc.risq.qc.ca!newsflash.concordia.ca!not-for-mail From: Riccardo Telaro Newsgroups: bionet.software Subject: E. Coli gene sequencing software Date: Sat, 07 Feb 1998 12:56:47 -0500 Organization: Concordia University Lines: 40 Message-ID: <34DCA05F.379BE0F9@alcor.concordia.ca> NNTP-Posting-Host: alcor.concordia.ca Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------DEABDDBA2553373F223784A1" NNTP-Posting-User: r_telar X-Mailer: Mozilla 4.04 [en] (Win95; I) --------------DEABDDBA2553373F223784A1 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi there, I'm looking for some good interesting Windows 95 software on molecular biological techniques. I'm currently working on a project which has to do with cloning and sequencing the Gal P gene in E. Coli. Can any one suggest me a program that will conduct restriction analysis, mapping, vector usage and so on all in one program. Thanx --------------DEABDDBA2553373F223784A1 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit

Hi there,

I'm looking for some good interesting Windows 95 software on molecular biological techniques.

I'm currently working on a project which has to do with cloning and sequencing the Gal P gene in E. Coli.

Can any one suggest me a program that will conduct restriction analysis, mapping, vector usage and so on all in one program.

Thanx --------------DEABDDBA2553373F223784A1-- From owner-software@net.bio.net Fri Feb 06 22:00:00 1998 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.software Subject: Recomb98: student financial support Date: 6 Feb 1998 16:16:33 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802070014.QAA08378@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net Thanks to the generosity of our governmental and corporate sponsors, limited financial support for travel expenses will be available for students attending RECOMB 98. Support is offered on a competitive basis. In order to apply for financial support, you must: 1) be a graduate student or undergraduate student attending RECOMB 98, 2) register for RECOMB 98 including the submission of registration fees by Feb. 20, 1998, 3) submit a one page essay describing why you should receive financial support. The essay (up to *500* words) should include the following information: i) your name, ii) your email address, iii) the school you are attending, iv) the professor who is overseeing your research, v) a short description of your research, vi) the paper title if you have a paper at RECOMB 98, v) a short description of your research, vi) the paper title if you have a paper at RECOMB 98, vii) the poster title if you have a poster at RECOMB 98, viii) any other information that you think would be relevant. The essay should be sent via email to support@ecology.biomath.mssm.edu by Feb. 20, 1998. Those students selected for financial support will be notified by email on or before March 9, 1998. Early registration ends February 20, 1998! Hotel conference rate ends February 24, 1998! From owner-software@net.bio.net Fri Feb 06 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!logbridge.uoregon.edu!arclight.uoregon.edu!news.cc.ukans.edu!not-for-mail From: Mousheng Xu Newsgroups: bionet.software Subject: UPDATE: Bioinformation Search Center 4.0 Date: Sat, 07 Feb 1998 16:54:19 -0600 Organization: University of Kansas Computing Services Lines: 27 Message-ID: <34DCE61B.FF6@eecs.ukans.edu> NNTP-Posting-Host: blizzard.rsl.ukans.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; OSF1 V4.0 alpha) Dear Scientists: The Bioinformation Search Center (BSC) 4.0 (http://www.ittc.ukans.edu/~mxu/cgi-bin/thesis/bi.cgi) is now available to the public! Major new features of Version 4.0: 1. Short words are allowed for search. For example, in the previous versions of BSC, the "IX" of "human factor IX" was not used in search, but in BSC 4.0, it is used. 2. Keywords are highlighted in the results. Major known problem: Common words are not used for search in BSC. For the above example, both "human" and "factor" are so common that they are not used for search. In this case, it is bad. But a lot of common words such as "the", "a", "an" are surely bad in search of biological information. This problem can easily be solved, technically. But it takes programmer's time and the university's computer disk space. Please give this baby a try! Any comments are highly appreciated! Please see below for the brief introduction to BSC. Thanks a lot. Sincerely, Mousheng Xu From owner-software@net.bio.net Fri Feb 06 22:00:00 1998 Path: biosci!agate!ihnp4.ucsd.edu!sdd.hp.com!vixen.cso.uiuc.edu!news2.chicago.iagnet.net!qual.net!iagnet.net!203.29.160.2!ihug.co.nz!clear.net.nz!news.hn.netlink.co.nz!canterbury.ac.nz!not-for-mail From: Mark Silby Newsgroups: bionet.software Subject: Helix-Turn-Helix Date: Sun, 08 Feb 1998 10:32:40 -0800 Organization: University of Canterbury Lines: 13 Message-ID: <34DDFA48.27A1@student.canterbury.ac.nz> NNTP-Posting-Host: 132.181.220.90 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win16; I) Hi all I am investigating a putative DNA binding protein, and am interested in aquiring a program that can be used to predict helix-turn-helix motifs based upon the predicted protein sequence. Any suggestions of shareware or commercial programs would be appreciated. Cheers, Mark Silby Department of Plant and Microbial Sciences University of Canterbury Christchurch New Zealand. From owner-software@net.bio.net Fri Feb 06 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!arclight.uoregon.edu!news.cc.ukans.edu!not-for-mail From: Mousheng Xu Newsgroups: bionet.software Subject: !!! HELP-SURVEY-BONUS: BSC 4.0 !!! Date: Sat, 07 Feb 1998 17:01:51 -0600 Organization: University of Kansas Computing Services Lines: 9 Message-ID: <34DCE7DF.52BF@eecs.ukans.edu> NNTP-Posting-Host: blizzard.rsl.ukans.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; OSF1 V4.0 alpha) Dear Scientists: Please see my last post titled as "UPDATE: Bioinformation Search Center 4.0" for introduction about 4.0. The one who finishes the survey of BSC will get the following bonus: 1. Core codes of the whole BSC system. 2. My thanks to you. -- Mousheng Xu From owner-software@net.bio.net Sat Feb 07 22:00:00 1998 From: "John Taylor" Subject: Card Collecting Software Message-ID: <01bd342c$53963440$3d442499@gobraves> X-Newsreader: Microsoft Internet News 4.70.1155 Newsgroups: bionet.software Date: Sat, 07 Feb 1998 16:55:02 -0800 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!207.68.152.12!upnetnews01!upnetnews03 Lines: 12 Hi, if you have time please go to http://www.picknclick.com and download the demo version of this software. It's called The Ultimate Card Collector! and it's software that card collectors can use to get organized. There are over 170,000 preloaded cards that help to cut down on manual entries. The software also has the ability to create a shopping list of cards you are missing and it will let you do a lot of other things. Regards, John Taylor From owner-software@net.bio.net Sat Feb 07 22:00:00 1998 Path: biosci!agate!howland.erols.net!Supernews73!supernews.com!Supernews69!not-for-mail From: "Andrew Miller" Newsgroups: bionet.software Subject: free medical image 3D visualization software for Windows95/NT Date: Sun, 8 Feb 1998 12:22:31 -0500 Organization: All USENET -- http://www.Supernews.com Lines: 18 Message-ID: <6bkq0s$akd$1@usenet50.supernews.com> NNTP-Posting-Host: 10893@206.30.88.62 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Just to let you know, There's a freeware application for Windows95/NT called NeuroModeller (version 1.09) developed by Cornell Medical Center, Division of Neurosurgery, that allows 3D reconstruction of medical slice images. Available for download at: http://users.infohouse.com/amiller/home.htm ... approximately 640 KB in size. Currently reads DICOM and BMP slice file fomats. Sincerely, Andrew Miller, MD amiller@infohouse.com From owner-software@net.bio.net Sat Feb 07 22:00:00 1998 Path: biosci!agate!howland.erols.net!woodstock.news.demon.net!demon!dispose.news.demon.net!demon!peer.news.zetnet.net!zetnet.co.uk!user-10002114.zetnet.co.uk!not-for-mail From: Garth Williams Newsgroups: bionet.software Subject: Re: PC as answeringmachine? Date: Fri, 6 Feb 1998 23:14:42 GMT Message-ID: <1998020623144271355@zetnet.co.uk> References: <01bd330c$67d0c040$LocalHost@aplusr> NNTP-Posting-Host: user-10002114.zetnet.co.uk X-Mailer: ZIMACS Version 1.20c 10002114 Lines: 31 The message <01bd330c$67d0c040$LocalHost@aplusr> from "joris" contains these words: > Does anyone know of software available which can make a pc and modem work > as an answeringmachine, including soundrecording (for instance in *.wav > files)? > I would be very grateful for an answer and/or a tip. > Thanks a lot, > Joris. Hi Joris, The Quicklink message centre software supplied as standard with my USR sportster external modem about 18 months ago includes options to set the modem and pc up as an answering machine. The modem includes a small internal microphone which is adequate to record an answering machine message. The software can be set up for multiple mailboxes, such as "Press 1 for sales, 2 for orders" etc. as well. The PC can be left on "listening" to the phone, and will respond to incoming calls ok. Regards, -- Garth Williams, Worcester. email: garth.williams@zetnet.co.uk www: http://www.users.zetnet.co.uk/jgw.computing/ From owner-software@net.bio.net Sun Feb 08 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!howland.erols.net!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news.mu-luebeck.de!not-for-mail From: "Lars Komorowski" Newsgroups: bionet.software Subject: Driver for Pharmacia HPLCManager 3.0 Date: Mon, 9 Feb 1998 14:12:48 +0100 Organization: Med. Universitaet zu Luebeck Lines: 5 Message-ID: <6bmvk4$hhi$1@gwsun.medinf.mu-luebeck.de> NNTP-Posting-Host: 141.83.167.168 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 I need printer drivers for HPLCManager 3.0 from Pharmacia for DOS. Who has got the installation disks ? Lars Komorowski From owner-software@net.bio.net Sun Feb 08 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!howland.erols.net!news.starnet.net!newsreader.wustl.edu!not-for-mail From: Sean Eddy Newsgroups: bionet.software Subject: Re: annotating EST sequence information with BLAST search output Date: 09 Feb 1998 07:46:31 -0600 Organization: Washington University in St. Louis Lines: 35 Message-ID: References: <199802090426.XAA02664@borduas.nlm.nih.gov> NNTP-Posting-Host: wrasse.wustl.edu X-Newsreader: Gnus v5.3/Emacs 19.34 francis@BORDUAS.NLM.NIH.GOV (Francis Ouellette) writes: > Why would one one to annotate any record with information > which will be out of date the day it is printed? > > I think we would want to discourage such annotations. That's a valid point. But on the other hand, in many cases, the annotation is useful, and much of the information does not go out of date. For example, if an EST has a 100% identity hit to a known gene, that information is not going to change. A less clear case, but also useful: if an EST shows a blastx hit against a well-known protein family (say, a transcription factor family), that's also useful information, even if we don't know yet exactly what gene the EST corresponds to. > If you want to see what the record is related to, see the > blast similarity which are computed in dbEST or in the related > sequences to a record present in Entrez. Loooking at > annotations which will never be updated is missleading, > and uninformative. That's too strong a position to take, I think. Scanning EST description lines is far, far faster than clicking through to see a whole dbEST record for each EST. Description lines should contain our "best effort" to give a short description of the EST. It's a user education problem to make sure people realize that those description lines are bound to be outdated, and that they may be misleading. But "uninformative" they're not, in my opinion. - Sean From owner-software@net.bio.net Sun Feb 08 22:00:00 1998 Path: biosci!prospect.anprod.csiro.au!d.adelson From: d.adelson@prospect.anprod.csiro.au (Dave Adelson) Newsgroups: bionet.software Subject: annotating EST sequence information with BLAST search output Date: 8 Feb 1998 19:49:32 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <9802090345.AA15455@nugget.prospect.anprod.CSIRO.AU> NNTP-Posting-Host: net.bio.net G'day, Does anyone know of a program similar to dfblast, which takes the BLAST output and uses it to annotate the original query sequence? I have dblast, but can't make it do what it is supposed to. Please cc replies to my email address as I do not always get the time to check USENET. Cheers, Dave David Adelson, PhD -- Senior Research Scientist CSIRO Division of Animal Production, Prospect, NSW, Australia Tel: +61 2 9840 2860 Fax: +61 2 9840 2939 All opinions are my own, not CSIRO's From owner-software@net.bio.net Sun Feb 08 22:00:00 1998 Path: biosci!HYDRUS.CC.UNIUD.IT!cism From: cism@HYDRUS.CC.UNIUD.IT (organizers) Newsgroups: bionet.software Subject: school-workshop announcement Date: 9 Feb 1998 10:25:09 -0800 Organization: CISM Lines: 140 Sender: daemon@net.bio.net Distribution: world Message-ID: <34DF498D.3422@hydrus.cc.uniud.it> NNTP-Posting-Host: net.bio.net School-Workshop on COMPUTATIONAL BIOLOGY June 10-19, 1998 CISM, Udine, Italy sponsored by Italian National Research Council UNESCO University of Udine ---------------------------------------------------------------------------- <*> General description <*> Program <*> Call for papers <*> Information <*> Organizing committee ---------------------------------------------------------------------------- General description In the past few years, Computational Molecular Biology has emerged as a prominent new active area of research, lying on the boundary of computer science, mathematics, operations research, statistics and, of course, molecular biology. Among the many problems studied in Computational Molecular Biology we find * Genomic data search problems ( -> Stringology and Statistics ) * DNA rearrangement problems ( -> Combinatorial Analysis ) * Sequence alignment problems ( -> Combinatorial Optimization ) * Construction of phylogenies ( -> Graph Theory ) The aim of this school is at providing a review of the most important computational problems motivated by different applications in molecular biology. In particular, results will be presented concerning the complexity of the problems, provably good and/or efficient solutions, modeling and statistical analysis. The school will last six days. The last two days will be devoted to a workshop where contributed papers will be presented. ---------------------------------------------------------------------------- Program * Basic concepts of molecular biology: R. Ravi - Carnegie Mellon University - Pittsburgh; * Computational challenges in gene-hunting: Pavel Pevzner - University of Southern California - Los Angeles; * Physical Mapping: Richard Karp - University of Washington - Seattle; * Sequence assembly: Eugene Myers - University of Arizona - Tucson; * Indexing Data Structures for Large Genomic DataBases: Paolo Ferragina - University of Pisa; * Algorithmic aspects of sequence comparison: Daniel Gusfield - University of California - Davis; * Pattern Matching Algorithms for Sequence Regularities and Statistics: Alberto Apostolico - University of Padua and Purdue University - West Lafayette; * Multiple sequence alignments: John Kececioglu - University of Georgia - Athens; * Phylogenetic reconstruction: Martin Farach - Rutgers University - Piscataway ; * Integrating phylogenetic reconstruction and multiple sequence alignments: Martin Vingron - Heidelberg; * Protein Folding and Structure Prediction Algorithms : Sorin Istrail - Sandia National Laboratories; * Shortest Paths, Hidden Markov Models and Weighted Automata: Raffaele Giancarlo - University of Palermo; ---------------------------------------------------------------------------- Call for papers The last two days of the school-workshop will be devoted to contributed lectures. Prospective lecturers are encouraged to submit by email an extended abstract (up to four pages long), in postscript format, to any of the organizers. Software presentations are also encouraged. The deadline for submissions is February 28, 1998. ---------------------------------------------------------------------------- Information Registration The registration fee is of 500,000 Italian lire, before March 31, 1998. A late fee of 650,000 Italian lire applies after March 31, 1998. A limited amount of scholarships will be available for participants in need of financial support. Priority will be given to participants from eastern european countries or developing countries. Applicants should send a CV to the organizing committee by March 31, 1998. * Click here for an ASCII version of the registration form. * Click here for an HTML version of the registration form. * Click here for info on financial support. Travel information Udine is located in Friuli Venezia Giulia, North-East of Italy, 70 kilometers from Trieste and 110 kilometers from Venice. Here is a list of hotels and a map of the city. Traveling by air: The nearest airport is Trieste Airport, located 40 kilometers from Udine. There are daily connections to/from Rome and Milan, and from Munich, Germany. A bus shuttle service to Udine is available in connection to these flights. In alternative to Udine Airport, there is Venice Airport, located 110 kilometers from Udine. From Venice-Mestre railway station there are several trains to Udine. Traveling by train: Udine can be reached from anywhere in Italy by train. The following link provides a time table of daily trains in Italy. Or, click on this link for a time table of trains between European countries . Contact address: Segreteria CISM, Piazza Garibaldi 18, 33100 Udine. Tel. +39-432-294989. Fax +39-432-501523. Email: cism@hydrus.cc.uniud.it ---------------------------------------------------------------------------- Organizing committee The coordinators of the School-Workshop are: * R. Ravi - Carnegie Mellon Universiy- Pittsburgh * P. Serafini - University of Udine * G. Lancia - University of Padova -------------------------------------- <*> Back to CISM home page From owner-software@net.bio.net Sun Feb 08 22:00:00 1998 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.software Subject: Recomb98: Deadlines & Preliminary Program Date: 9 Feb 1998 11:08:07 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 356 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802091906.LAA01480@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net Early registration ends February 20, 1998! Hotel conference rate ends February 24, 1998! For more details please visit our web site: http://www.mssm.edu/biomath/recomb98.html ---------------------------------------------------------------------------- RECOMB 98 SCHEDULE Saturday, March 21, 1998 7:00 pm - 10:00 pm Welcome Reception Renaissance Room Sunday, March 22, 1998 8:45 am Opening Remarks Embassy Ballroom Pavel Pevzner, RECOMB 1998 Program Committee Chair Gary Benson, RECOMB 1998 Conference Chair Sorin Istrail, RECOMB 1999 Program Committee Chair 9:00 am Distinguished New Technologies Lecture Pavel Pevzner, Chair David Cox The Human Genetic Variation: Oligonucleotide Chips and Human Disease 10:00 am Break Session 1, Chair: Martin Vingron 10:10 am Identifying Satellites in Nucleic Acid Sequences M. Sagot, G. Meyers 10:35 am Genome Analysis Using Clusters of Orthologous Groups (COGs) E. Koonin, R. Tatusov, M. Y. Galperin, M. N. Rozanov 11:00 am Break Session 2, Chair: Gene Myers 11:15 am Non-Adjoining Correlations Within Signals in DNA P. Agarwal and V. Bafna 11:40 am An Algorithm for Finding Tandem Repeats of Unspecified Pattern Size G. Benson 12:05 pm Lunch 1:30 pm Invited Lecture Session Sorin Istrail, Chair Charles Cantor Enhancements in Sequence Analysis With DNA Arrays 2:30 pm Break Session 3, Chair: Gary Benson 2:40 pm Motif Discovery in Biological Sequences Without Alignment or Enumeration I. Rigoutsos, A. Floratos 3:05 pm An Algorithm for Finding Novel Gapped Motifs in DNA Sequences E. Rocke, M. Tompa 3:30 pm A Polyhedral Approach to RNA Sequence Structure Alignment H. Lenhof, K. Reinert, M. Vingron 3:55 pm Break 4:10 pm Stanislav Ulam Computational Biology Address Michael Waterman, Chair Joshua Lederberg 8:00 pm-10:00 pm Business Meeting Renaissance Room Monday, March 23, 1998 Embassy Ballroom 9:00 am Distinguished Conference Lecture Richard Karp, Chair Ron Davis Whole Genome Analysis: Expression, Replication, Recombination, Allelic Variation, and Drug Discovery Function 10:00 am Break Session 4, Chair: David Searls 10:10 am Assessment of Ab Initio Protein Structure Prediction A. M. Lesk 10:35 am A Self-Consistent Field Optimization Approach to Build Energetically and Geometrically Correct Lattice Models of Proteins B. A. Reva, A. V. Finkelstein, J. Skolnick 11:00 am Break 11:15 am Modeling DNA Shuffling F. Sun 11:40 am Multiple Genome Rearrangements D. Sankoff, M. Blanchette 12:05 pm Lunch 1:30 pm Invited Lecture Session Eugene Koonin, Chair Ruben Abagyan Challenges of biomolecular structure prediction 2:30 pm Break Session 5, Chair: Martin Farach 2:40 pm From Four-taxon Trees to Phylogenies: The Case of Mammalian Evolution A. Ben-Dor, B. Chor, D. Graur, R. Ophir, D. Pelleg 3:05 pm On Reconstructing Species Trees From Gene Trees In Term of Duplications B. Ma, M. Li, L. Zhang 3:30 pm The Ordinal Quartet Method P. E. Kearney 3:55 pm Break 4:10 pm Invited Lecture Session Bonnie Berger, Chair Michael Levitt Bridging the Gap Between Sequence and Structure 6:00 pm-10:00 pm Poster Session Renaissance Room Tuesday, March 24, 1998 Embassy Ballroom 9:00 am Invited Lecture Session Ron Shamir, Chair David Schwartz New Approaches to Genomic Analaysis Using Single Molecules 10:00 am Break Session 6, Chair: Minoru Kanehisa 10:10 am Algorithms for Optical Mapping R. M. Karp, R. Shamir 10:35 am Estimation for Restriction Sites Observed by Optical Mapping Using Reversible-jump Markov Chain Monte Carlo J. K. Lee, V. Dancik, M. S. Waterman 11:00 am Break 11:15 am Partitioning K Clones: Hardness Results and a Practical Solution to the K-Popultaion Problem L. Parida, B. Mishra 11:40 am Constructing Maps Using the Span and Inclusion Relations D. Fasulo, T. Jiang, R. M. Karp, N. Sharma 12:05 pm Lunch 1:30 pm Invited Lecture Session Webb Miller, Chair John Yates Mass spectrometry and the proteome 2:30 pm Break Session 7, Chair: Thomas Lengauer 2:40 pm How Fast a Protein Chain Can Fold to Its Most Stable Structure? A. V. Finkelstein, A. Ya. Badretdinov 3:00 pm Algorithmic Determination of Core Positions in the VL and VH Domains of Immunoglobulin Molecules I. Gelfand, A. Kister, C. Kulikowski, O. Stoyanov 3:30 pm Alignments Without Low-Scoring Regions Z. Zhang, P. Berman, W. Miller 3:55 pm Dynamic Programmimg Alignment Accuracy I. Holmes and R. Durbin 4:20 pm Break 4:30 pm Invited Lecture Session David Haussler, Chair Klaus Gubernator Evolutionary drug discovery Wednesday, March 25, 1998 Embassy Ballroom Session 8, Chair: Dan Gusfield 8:30 am Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete B. Berger, T. Leighton 8:55 am On the Complexity of Protein Folding P. Crescenzi, D. Goldman, C. Papadimitriou, A. Piccolboni, M. Yannakakis 9:20 am A New Method for Modeling and Solving the Protein Fold Recognition Problem Y. Xu, D. Xu, E. C. Uberbacher 9:45 am Optimal Detection of Sequence Similarity by Local Alignment T. Hwa, M. Lassig 10:10 am Break Session 9, Chair: Terry Speed 10:20 am A Formally Exact Method to Numerically Analyze Local Denaturation in Superhelical DNA R. M. Fye, C. J. Benham 10:45 am The Theoretical Limits of DNA Sequence Discrimination of Polyamides W. L. Walker, D. S. Goodsell, E. M. Landaw 11:10 am Maxwell Demon and Topology Simplification by Type II Topoisomerases A. Vologodskii 11:35 am A Unified Approach to Word Statistics M. Regnier 12:00 pm Lunch Session 10, Chair: Phil Green 1:00 pm Regression Analysis of Multiple Protein Structures T. D. Wu, S. C. Schmidler, T. Hastie, D. L. Brutlag 1:25 pm Better Methods for Solving Parsimony and Compatiblity M. Bonet, M. Steel, T. Warnow, S. Yooseph 1:50 pm Beyond Mutation Matrices: Physical-Chemistry Based Evolutionary Models J. M. Koshi, D. P. Mindell, R. A. Goldstein 2:15 pm A Structure Based Similarity Measure for Nucleic Acid Sequence Comparison R. Liu, T. W. Blackwell and D. J. States 2:40 pm Break Session 11, Chair: David Benson 2:55 pm The Hierarchical Organization of Molecular Structure Computations C. C. Chen, J. P. Singh, R. B. Altman 3:20 pm Estimaiton of Allele Frequencies From Color-Multiplexed Electropherograms D. G. Politte, D. R. Maffitt, D. J. States 3:45 pm Analysis of the Position Dependent Amino Acid Probabilities and its Applicationts to the Search for Remote Homologues S. R. Sunyaev, I. V. Rodchenkov, F. Eisenhaber, E. N. Kuznetsov 4:10 pm Family-based Homology Detection via Pairwise Sequence Comparison W. N. Grundy End of RECOMB 98 From owner-software@net.bio.net Sun Feb 08 22:00:00 1998 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.software Subject: Recomb98: Deadlines & Preliminary Program Date: 9 Feb 1998 11:07:48 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 356 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802091906.LAA01478@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net Early registration ends February 20, 1998! Hotel conference rate ends February 24, 1998! For more details please visit our web site: http://www.mssm.edu/biomath/recomb98.html ---------------------------------------------------------------------------- RECOMB 98 SCHEDULE Saturday, March 21, 1998 7:00 pm - 10:00 pm Welcome Reception Renaissance Room Sunday, March 22, 1998 8:45 am Opening Remarks Embassy Ballroom Pavel Pevzner, RECOMB 1998 Program Committee Chair Gary Benson, RECOMB 1998 Conference Chair Sorin Istrail, RECOMB 1999 Program Committee Chair 9:00 am Distinguished New Technologies Lecture Pavel Pevzner, Chair David Cox The Human Genetic Variation: Oligonucleotide Chips and Human Disease 10:00 am Break Session 1, Chair: Martin Vingron 10:10 am Identifying Satellites in Nucleic Acid Sequences M. Sagot, G. Meyers 10:35 am Genome Analysis Using Clusters of Orthologous Groups (COGs) E. Koonin, R. Tatusov, M. Y. Galperin, M. N. Rozanov 11:00 am Break Session 2, Chair: Gene Myers 11:15 am Non-Adjoining Correlations Within Signals in DNA P. Agarwal and V. Bafna 11:40 am An Algorithm for Finding Tandem Repeats of Unspecified Pattern Size G. Benson 12:05 pm Lunch 1:30 pm Invited Lecture Session Sorin Istrail, Chair Charles Cantor Enhancements in Sequence Analysis With DNA Arrays 2:30 pm Break Session 3, Chair: Gary Benson 2:40 pm Motif Discovery in Biological Sequences Without Alignment or Enumeration I. Rigoutsos, A. Floratos 3:05 pm An Algorithm for Finding Novel Gapped Motifs in DNA Sequences E. Rocke, M. Tompa 3:30 pm A Polyhedral Approach to RNA Sequence Structure Alignment H. Lenhof, K. Reinert, M. Vingron 3:55 pm Break 4:10 pm Stanislav Ulam Computational Biology Address Michael Waterman, Chair Joshua Lederberg 8:00 pm-10:00 pm Business Meeting Renaissance Room Monday, March 23, 1998 Embassy Ballroom 9:00 am Distinguished Conference Lecture Richard Karp, Chair Ron Davis Whole Genome Analysis: Expression, Replication, Recombination, Allelic Variation, and Drug Discovery Function 10:00 am Break Session 4, Chair: David Searls 10:10 am Assessment of Ab Initio Protein Structure Prediction A. M. Lesk 10:35 am A Self-Consistent Field Optimization Approach to Build Energetically and Geometrically Correct Lattice Models of Proteins B. A. Reva, A. V. Finkelstein, J. Skolnick 11:00 am Break 11:15 am Modeling DNA Shuffling F. Sun 11:40 am Multiple Genome Rearrangements D. Sankoff, M. Blanchette 12:05 pm Lunch 1:30 pm Invited Lecture Session Eugene Koonin, Chair Ruben Abagyan Challenges of biomolecular structure prediction 2:30 pm Break Session 5, Chair: Martin Farach 2:40 pm From Four-taxon Trees to Phylogenies: The Case of Mammalian Evolution A. Ben-Dor, B. Chor, D. Graur, R. Ophir, D. Pelleg 3:05 pm On Reconstructing Species Trees From Gene Trees In Term of Duplications B. Ma, M. Li, L. Zhang 3:30 pm The Ordinal Quartet Method P. E. Kearney 3:55 pm Break 4:10 pm Invited Lecture Session Bonnie Berger, Chair Michael Levitt Bridging the Gap Between Sequence and Structure 6:00 pm-10:00 pm Poster Session Renaissance Room Tuesday, March 24, 1998 Embassy Ballroom 9:00 am Invited Lecture Session Ron Shamir, Chair David Schwartz New Approaches to Genomic Analaysis Using Single Molecules 10:00 am Break Session 6, Chair: Minoru Kanehisa 10:10 am Algorithms for Optical Mapping R. M. Karp, R. Shamir 10:35 am Estimation for Restriction Sites Observed by Optical Mapping Using Reversible-jump Markov Chain Monte Carlo J. K. Lee, V. Dancik, M. S. Waterman 11:00 am Break 11:15 am Partitioning K Clones: Hardness Results and a Practical Solution to the K-Popultaion Problem L. Parida, B. Mishra 11:40 am Constructing Maps Using the Span and Inclusion Relations D. Fasulo, T. Jiang, R. M. Karp, N. Sharma 12:05 pm Lunch 1:30 pm Invited Lecture Session Webb Miller, Chair John Yates Mass spectrometry and the proteome 2:30 pm Break Session 7, Chair: Thomas Lengauer 2:40 pm How Fast a Protein Chain Can Fold to Its Most Stable Structure? A. V. Finkelstein, A. Ya. Badretdinov 3:00 pm Algorithmic Determination of Core Positions in the VL and VH Domains of Immunoglobulin Molecules I. Gelfand, A. Kister, C. Kulikowski, O. Stoyanov 3:30 pm Alignments Without Low-Scoring Regions Z. Zhang, P. Berman, W. Miller 3:55 pm Dynamic Programmimg Alignment Accuracy I. Holmes and R. Durbin 4:20 pm Break 4:30 pm Invited Lecture Session David Haussler, Chair Klaus Gubernator Evolutionary drug discovery Wednesday, March 25, 1998 Embassy Ballroom Session 8, Chair: Dan Gusfield 8:30 am Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete B. Berger, T. Leighton 8:55 am On the Complexity of Protein Folding P. Crescenzi, D. Goldman, C. Papadimitriou, A. Piccolboni, M. Yannakakis 9:20 am A New Method for Modeling and Solving the Protein Fold Recognition Problem Y. Xu, D. Xu, E. C. Uberbacher 9:45 am Optimal Detection of Sequence Similarity by Local Alignment T. Hwa, M. Lassig 10:10 am Break Session 9, Chair: Terry Speed 10:20 am A Formally Exact Method to Numerically Analyze Local Denaturation in Superhelical DNA R. M. Fye, C. J. Benham 10:45 am The Theoretical Limits of DNA Sequence Discrimination of Polyamides W. L. Walker, D. S. Goodsell, E. M. Landaw 11:10 am Maxwell Demon and Topology Simplification by Type II Topoisomerases A. Vologodskii 11:35 am A Unified Approach to Word Statistics M. Regnier 12:00 pm Lunch Session 10, Chair: Phil Green 1:00 pm Regression Analysis of Multiple Protein Structures T. D. Wu, S. C. Schmidler, T. Hastie, D. L. Brutlag 1:25 pm Better Methods for Solving Parsimony and Compatiblity M. Bonet, M. Steel, T. Warnow, S. Yooseph 1:50 pm Beyond Mutation Matrices: Physical-Chemistry Based Evolutionary Models J. M. Koshi, D. P. Mindell, R. A. Goldstein 2:15 pm A Structure Based Similarity Measure for Nucleic Acid Sequence Comparison R. Liu, T. W. Blackwell and D. J. States 2:40 pm Break Session 11, Chair: David Benson 2:55 pm The Hierarchical Organization of Molecular Structure Computations C. C. Chen, J. P. Singh, R. B. Altman 3:20 pm Estimaiton of Allele Frequencies From Color-Multiplexed Electropherograms D. G. Politte, D. R. Maffitt, D. J. States 3:45 pm Analysis of the Position Dependent Amino Acid Probabilities and its Applicationts to the Search for Remote Homologues S. R. Sunyaev, I. V. Rodchenkov, F. Eisenhaber, E. N. Kuznetsov 4:10 pm Family-based Homology Detection via Pairwise Sequence Comparison W. N. Grundy End of RECOMB 98 From owner-software@net.bio.net Sun Feb 08 22:00:00 1998 Path: biosci!BORDUAS.NLM.NIH.GOV!francis From: francis@BORDUAS.NLM.NIH.GOV (Francis Ouellette) Newsgroups: bionet.software Subject: Re: annotating EST sequence information with BLAST search output Date: 8 Feb 1998 20:28:46 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802090426.XAA02664@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net > From: d.adelson@prospect.anprod.csiro.au (Dave Adelson) > Subject: annotating EST sequence information with BLAST search output > Does anyone know of a program similar to dfblast, which > takes the BLAST output and uses it to annotate the > original query sequence? Why would one one to annotate any record with information which will be out of date the day it is printed? I think we would want to discourage such annotations. If you want to see what the record is related to, see the blast similarity which are computed in dbEST or in the related sequences to a record present in Entrez. Loooking at annotations which will never be updated is missleading, and uninformative. regards, francis -- | B.F. Francis Ouellette | GenBank Coordinator | | francis@ncbi.nlm.nih.gov From owner-software@net.bio.net Sun Feb 08 22:00:00 1998 Path: biosci!MAIL.CYBERLINK.BG!anastas From: anastas@MAIL.CYBERLINK.BG (Anastas Pashov) Newsgroups: bionet.software Subject: Reading Mac disks in PC Date: 9 Feb 1998 15:06:40 -0800 Organization: none Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <34D89294.509B@mail.cyberlink.bg> Reply-To: anastas@mail.cyberlink.bg NNTP-Posting-Host: net.bio.net Hello, Does anyone know of freeware for reading Mac disks in PC? Thanx in advance! Anastas Pashov From owner-software@net.bio.net Sun Feb 08 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news-peer-west.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.wli.net!pln!spln!extra.newsguy.com!newsp.newsguy.com!enews1 From: No@Spam.please (Rick Thompson) Newsgroups: bionet.software Subject: ImageQuant for NT can it run under Win95? Date: 9 Feb 1998 18:51:14 GMT Organization: None Lines: 15 Message-ID: <6bnj72$i70@enews1.newsguy.com> NNTP-Posting-Host: p-335.newsdawg.com X-Newsreader: WinVN 0.99.9 (Released Version) (x86 32bit) We have a Storm PhophoImager system running imagequant software for windows NT. The old version of ImageQuant for windows 3.3 will run under Win95, but is limited in that it does not have many of the features of the NT version. Especially it does not support long file names. I'd like to know if anyone out there has figured out a way to get the NT version to run under Win95. This would free up a logjam on the NT work station. Unfortunately Molecular Dynamics simply states `it was designed to run under NT' and no one here is really experienced with cross platform apps. This might be simple (e.g. copy a few DLLs with appropriate path statements), or it might be impossible for all I know. If anyone has any experience or ideas I'd appreciate hearing them. You can contact me directly at: Richard.Thompson*at*uc.edu From owner-software@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!NCBI.NLM.NIH.GOV!francis From: francis@NCBI.NLM.NIH.GOV Newsgroups: bionet.software Subject: Re: annotating EST sequence information with BLAST search output Date: 9 Feb 1998 17:47:15 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 61 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802100142.UAA06140@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net > To: bio-soft@net.bio.net > From: Sean Eddy > Subject: Re: annotating EST sequence information with BLAST search output > Date: 09 Feb 1998 07:46:31 -0600 > francis@BORDUAS.NLM.NIH.GOV (Francis Ouellette) writes: > > Why would one one to annotate any record with information > > which will be out of date the day it is printed? > > > > I think we would want to discourage such annotations. > > That's a valid point. But on the other hand, in many cases, the > annotation is useful, and much of the information does not go out of > date. true ... and this is probably why it's been so popular an activity. It's just that I'm not a great believer of automatic annotations ... > > If you want to see what the record is related to, see the > > blast similarity which are computed in dbEST or in the related > > sequences to a record present in Entrez. Loooking at > > annotations which will never be updated is missleading, > > and uninformative. > > That's too strong a position to take, yes, but it does elicit good press! :) > I think. Scanning EST > description lines is far, far faster than clicking through to see a > whole dbEST record for each EST. Description lines should contain our > "best effort" to give a short description of the EST. yes, I agree ... it is faster, but what I question is what does it mean when you find you have something which is similar to somothing which is imilar to a homologue of something else? > It's a user education problem to make sure people realize that those > description lines are bound to be outdated, and that they may be > misleading. But "uninformative" they're not, in my opinion. they can be, but I agree .. the buyer must be aware ... and as a 'seller', I definitly should tell people to be careful. ** ** Be careful when reading DEFINITION lines of EST records, they can be ** informative, but they can also be misleading, and/or out of date! ** regards to all, francis -- | B.F. Francis Ouellette | GenBank Coordinator | | francis@ncbi.nlm.nih.gov From owner-software@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!kyowa.co.jp!snakagawa From: snakagawa@kyowa.co.jp (Satoshi Nakagawa) Newsgroups: bionet.software Subject: About MACAW Date: 9 Feb 1998 17:41:36 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <34DFAFC4.56DF@kyowa.co.jp> NNTP-Posting-Host: net.bio.net Does anyone know of the MACAW that can make multiple sequence alignments? Can I use it on a local system? Thanks for your help. *********************************** Satoshi Nakagawa snakagawa@kyowa.co.jp Kyowa Hakko Kogyo. Co. Ltd. Tokyo Research Laboratories 3-6-6 Asahimachi Machida-shi Tokyo, Japan *********************************** From owner-software@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!news-peer.sprintlink.net!news-backup-west.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!204.97.16.5!news.monad.net!not-for-mail From: jkeenan@top.monad.net Newsgroups: bionet.software Subject: Software aids project planning Date: 10 Feb 1998 12:35:19 GMT Organization: MonadNet Lines: 8 Message-ID: <6bphi7$3rs$2@news.monad.net> NNTP-Posting-Host: tcr5-75.keene.monad.net X-Newsreader: AIR News 3.X (SPRY, Inc.) The Amazing DOS Thought Processor supports journalling, idea development, and no-fault thought entry. Runs on any pc. See user's guide and download actual (four-year) example at http://top.monad.net/~jkeenan (click on the "retro software") There's an order blank for this $29.95 program. From owner-software@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!Cabal.CESspool!bofh.vszbr.cz!newsfeed.eerie.fr!jussieu.fr!univ-lille1.fr!u-strasbg.fr!news From: pingouin@chouchen.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: DNA/Protein homology search Date: 10 Feb 1998 09:01:39 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 15 Message-ID: <6bp51j$3nb@news.u-strasbg.fr> References: <6bmm8s$s6$1@kadri.ut.ee> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: chouchen.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.8 In article <6bmm8s$s6$1@kadri.ut.ee>, mremm@tamm.eenet.ee (Maido Remm) writes: > 1. Query and target are DNA > 2. Translate both sequences correctly to protein sequence > 3. Align protein sequences > 4. Output the same alignment as DNA sequence Seems to be the job of tblastx, no? François. -- François Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France From owner-software@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!newsfeed.eerie.fr!jussieu.fr!univ-lille1.fr!u-strasbg.fr!news From: pingouin@chouchen.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: annotating EST sequence information with BLAST search output Date: 10 Feb 1998 08:58:57 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 50 Message-ID: <6bp4sh$3nb@news.u-strasbg.fr> References: <199802100142.UAA06140@borduas.nlm.nih.gov> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: chouchen.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.8 In article <199802100142.UAA06140@borduas.nlm.nih.gov>, francis@NCBI.NLM.NIH.GOV writes: > > true ... and this is probably why it's been so popular an activity. > It's just that I'm not a great believer of automatic annotations ... Sure, because, sometimes, the second record contains more information, and only a manual annotation would be useful in this case... > yes, I agree ... it is faster, but what I question is what does it mean > when you find you have something which is similar to somothing which is > imilar to a homologue of something else? Yep, and what is the real information you are looking for in an EST database? If you are looking for an homolog, you will find it in the nr database. Looking for homologs of homologs, is, like Francis says, quite a strange usage ;-). What is the real information you can find in a good EST database? For me : - Expression Pattern - Alternative splicing All the rest is quite unuseful. That's why I think that the good way to maintain an EST database is by clustering homolog ESTs, like STACKS do (but this implies better sequence quality or sequence cleaning). But probably, separatly, an expression database, a "size" or cluster analysis one (to find full-length sequences or alternative splicing), and whatever you would like. But the current repository process is not as useful as it could be. > ** > ** Be careful when reading DEFINITION lines of EST records, they can be > ** informative, but they can also be misleading, and/or out of date! > ** Hey! stop increasing the size of the database! ;-)))). Try to write it only with ATGCs, so we could compress it ;-). At least, end-user should finally stop using things without reading the docs... François (dreamin'). -- François Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France From owner-software@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!Cabal.CESspool!bofh.vszbr.cz!newsfeed.eerie.fr!jussieu.fr!univ-lyon1.fr!news.univ-aix.fr!not-for-mail From: Eric Blanc Newsgroups: bionet.software Subject: Re: Reading Mac disks in PC Date: Tue, 10 Feb 1998 09:06:52 +0100 Organization: Universites d' Aix en Provence Lines: 25 Message-ID: <34E00A9C.41C6@afmb.cnrs-mrs.fr> References: <34D89294.509B@mail.cyberlink.bg> NNTP-Posting-Host: afmb83.cnrs-mrs.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) Anastas Pashov wrote: > > Hello, > > Does anyone know of freeware for reading Mac disks in PC? > > Thanx in advance! > > Anastas Pashov I think: Mac-ette for DOS, and tm24u under win95 -- ------------------------------------------------------------------------------ Eric Blanc Webmaster for AFMB Email: eric@afmb.cnrs-mrs.fr WWW: http://afmb.cnrs-mrs.fr/~eric/ InPerson:eric@afmb83.cnrs-mrs.fr AFMB CNRS-UPR 9039 31 Ch J. Aiguier 13402 Marseille CEDEX 20 FRANCE Phone: 33-4-91-16-45-29 ------------------------------------------------------------------------------ From owner-software@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-feed.inet.tele.dk!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software Subject: Re: Web translation utility Date: Tue, 10 Feb 1998 13:23:18 +0000 Organization: EMBL - EBI Lines: 22 Message-ID: <34E054C6.7EEF1D4C@ebi.ac.uk> References: <199802051454.JAA12430@borduas.nlm.nih.gov> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX64 6.2 IP28) francis@NCBI.NLM.NIH.GOV wrote: > > > From BIOSCI-REQUEST@net.bio.net Thu Feb 5 09:42:05 1998 > > > Could someone point me to a web translation utility? I simply want to input a > > DNA sequence and (after defining the reading frame), get back the peptide > > sequence. Does NCBI have a utility like this? > > > > Answer by email, please sjhogart@unity.ncsu.edu Also, you could have a look at http://www2.ebi.ac.uk/translate/ -Heikki ______ _/ _/_____________________________________________________ _/ _/ http://www2.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From owner-software@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!Supernews60!supernews.com!uunet!in2.uu.net!news.pyramid.com!whowhere.com!nntp.csuchico.edu!waldorf.csc.calpoly.edu!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software Subject: Re: Helix-Turn-Helix Date: 9 Feb 1998 17:50:33 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 19 Message-ID: <6bnfl9$m4a@gap.cco.caltech.edu> References: <34DDFA48.27A1@student.canterbury.ac.nz> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu In article <34DDFA48.27A1@student.canterbury.ac.nz>, Mark Silby writes: >Hi all > >I am investigating a putative DNA binding protein, and am interested in >aquiring a program that can be used to predict helix-turn-helix motifs >based upon the predicted protein sequence. Any suggestions of shareware >or commercial programs would be appreciated. > The EGCG package contains a program HELIXTURNHELIX which may do what you want. Many sites that have GCG also have EGCG installed. The closest site that I know of to you is ANGUS, but probably somebody in NZ has these programs installed - ask around. Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-feed.inet.tele.dk!bofh.vszbr.cz!masternews.telia.net!news-stkh.gip.net!news.gsl.net!gip.net!news.kolumbus.fi!news.uninet.ee!kadri.ut.ee!tamm!mremm From: mremm@tamm.eenet.ee (Maido Remm) Newsgroups: bionet.software Subject: DNA/Protein homology search Date: 9 Feb 1998 10:37:16 GMT Organization: Estonian Biocentre Lines: 18 Message-ID: <6bmm8s$s6$1@kadri.ut.ee> NNTP-Posting-Host: tamm.ebc.ee Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: kadri.ut.ee 887020636 902 (None) 193.40.23.2 X-Complaints-To: usenet@kadri.ut.ee X-Newsreader: TIN [version 1.2 PL2] Hei, Has anybody written script or program to align gene DNA sequences according to their protein sequence: I mean it should do the following 1. Query and target are DNA 2. Translate both sequences correctly to protein sequence 3. Align protein sequences 4. Output the same alignment as DNA sequence I would name it codon alignment. It should have much more sense than straigth comparision of DNA. I have been told that similar program have announced here recently, but i was unable to find something like that in archives. Thanks for your time, Maido Remm Estonian Biocentre. From owner-software@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!agate!newsgate.duke.edu!news-relay.ncren.net!ussun2n!news@ussun2n.glaxo.com From: "Gary H. Merrill" Newsgroups: sci.med.informatics,comp.ai,comp.ia.nat-lang,bionet.software Subject: 2nd CFP: AAAI-98 Wkshp on Knowledge Sharing Across Bio and Med KB Systems Date: Tue, 10 Feb 1998 15:43:08 -0500 Organization: GlaxoWellcome Inc Lines: 125 Message-ID: <34E0BBDC.3F4D@glaxowellcome.com> Reply-To: ghm48805@glaxowellcome.com NNTP-Posting-Host: 152.51.45.146 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (WinNT; I) CC: dp33010@glaxowellcome.com, bean@nlm.nih.gov, abrass@manchester.ac.uk, hammo001@mc.duke.edu, jenders@cucis.cis.columbia.edu In addition to soliciting submissions from potential presenters, we encourage others interested in attending and taking part in the discussions to send a brief letter indicating their desire to attend. Please note that the deadline for submissions is March 11. ============== TITLE AAAI-98 Workshop on KNOWLEDGE SHARING ACROSS BIOLOGICAL AND MEDICAL KNOWLEDGE BASED SYSTEMS DATE AND LOCATION National Conference on Artificial Intelligence (AAAI-98) in Madison, Wisconsin, July 26 - July 27, 1998. See the AAAI web site at http://www.aaai.org for additional details. DESCRIPTION The amount of biological and medical information is growing at an exponential rate and overwhelming researchers and clinicians. Various groups have applied the technology of knowledge base systems to help in the effective utilization of available information. These systems have been used for applications in information retrieval, natural language processing, database integration, machine earning, data mining, and decision-making. While there is a substantial overlap of knowledge represented in these knowledge based systems there has been very limited dialog among the various groups creating these systems. This one-day workshop explores ways in which the knowledge contained in the various systems can be shared. Specifically, the workshop goals include: 1. Understanding the scope of knowledge contained in various knowledge based systems in biology and medicine. 2. Understanding strengths and limitations of different knowledge representation formalisms, inference engines, and knowledge acquisition methods for biological and medical systems. 3. Identifying strategies for knowledge sharing across different development groups as we move toward more comprehensive knowledge bases for researchers and clinicians in biology and medicine. SUBMISSIONS Potential presenters should submit a short paper (up to 5-8 pages) addressing any of the issues relevant to the workshop goals. Others interested in participating should submit a 1-2 page statement of background and interest. E-mail in PostScript or MS Word format to Dhiraj K. Pathak at dp33010@glaxowellcome.com or Gary H. Merrill at ghm48805@glaxowellcome.com Submission Deadline: March 11, 1998 Notification Date: April 1, 1998 ORGANIZING COMMITTEE Dhiraj K. Pathak, Glaxo Wellcome (Co-chair) (dp33010@glaxowellcome.com) Gary H. Merrill, Glaxo Wellcome (Co-chair) (ghm48805@glaxowellcome.com) Carol Bean, National Library of Medicine (bean@nlm.nih.gov) Andy Brass, University of Manchester (abrass@manchester.ac.uk) Ed Hammond, Duke University (hammo001@mc.duke.edu) Rober Jenders, Columbia University (jenders@cucis.cis.columbia.edu) -- Gary H. Merrill / Principal Consultant, Information Access Technology [Views and opinions expressed here are my own and not necessarily those of GlaxoWellcome Inc.] From owner-software@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!164.67.42.145!awabi.library.ucla.edu!134.139.1.31!csulb.edu!gatech!nntp-xfer.ncsu.edu!not-for-mail From: Burkhard Morgenstern Newsgroups: bionet.software Subject: Re: DNA/Protein homology search Date: Tue, 10 Feb 1998 09:38:43 -0500 Organization: North Carolina State University Lines: 34 Message-ID: <34E06673.4A9F@gsf.de> References: <6bmm8s$s6$1@kadri.ut.ee> NNTP-Posting-Host: poole.statgen.ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5.1 sun4u) Maido Remm wrote: > > Hei, > > Has anybody written script or program to align gene DNA sequences according > to their protein sequence: I mean it should do the following > > 1. Query and target are DNA > 2. Translate both sequences correctly to protein sequence > 3. Align protein sequences > 4. Output the same alignment as DNA sequence > > I would name it codon alignment. It should have much more sense than > straigth comparision of DNA. I have been told that similar program have > announced here recently, but i was unable to find something like that in > archives. > > Thanks for your time, > Maido Remm > Estonian Biocentre. Hello, I have written an alignment program that does exactly what you are looking for. It is called DIALIGN. Executables for various UNIX platforms (including LINUX) are available at http://www.gsf.de/biodv/dialign.html Hope this helps Burkhard Morgenstern From owner-software@net.bio.net Tue Feb 10 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!152.163.199.19!portc03.blue.aol.com!audrey02.news.aol.com!not-for-mail From: legalsuite@aol.com (LEGALSUITE) Newsgroups: bionet.software Subject: URGENT MESSAGE FOR USERS OF COREL SOFTWARE Date: 11 Feb 1998 18:58:33 GMT Lines: 20 Message-ID: <19980211185800.NAA24220@ladder02.news.aol.com> NNTP-Posting-Host: ladder02.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com Have you been lied to or deceived by Corel's technical team? Have they knowingly sold you the wrong software (Paradox 8) causing you to waste valueable time and money? Did you hire Corel's technical team to do a specific project for you and found that the finished product was defective or deceivingly incomplete? Did they complete you project months after the due date, or after months of being late, did they tell you that they did not have the technology to do your project at all, Or did they say that your project was complete when they had not even started the project that you hired them to do? Has Corel's technical team damaged your business or created great financial loss to your business? If you can prove any of the above statements and you are interested in joining a class action suite against Corel Corporation, contact me. Include a detailed description of your circumstances. LAWSUITE@aol.com From owner-software@net.bio.net Tue Feb 10 22:00:00 1998 From: classads@bigfoot.com (cda) Newsgroups: bionet.software Subject: need help..... Date: Wed, 11 Feb 1998 14:45:50 GMT Reply-To: classads@bigfoot.com Message-ID: <34e3a066.9464035@news.cyberway.com.sg> X-Newsreader: Forte Agent 1.5/32.451 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: 203.116.129.38 Lines: 14 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.direct.ca!Supernews60!supernews.com!uunet!in1.uu.net!newsfeed.attap.net!newsvr.cyberway.com.sg!cwaix!203.116.129.38 I am finding a real-life example in which the software development project was completes throught the use of prototyping. This is for my assignment, and I am having difficulties in finding such info over the net, so I've think of getting help from the usenet, from you people out there. Please send me the info , like URL where to find the information, your email address(to get contact with u). If you have experience this process yourself, please write to me the story including the following areas: - description of the software, its nature and application area; - a brieft write-up on the prototyping methodology of development; - why the prototyping method is particulaly suitable for the development of this software; - how the software was acctually developed using this methodology. From owner-software@net.bio.net Tue Feb 10 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!news-ge.switch.ch!iol!not-for-mail From: coupers@iol.ie (The Coupers) Newsgroups: bionet.software Subject: Text Comparison/ Version Software Date: Wed, 11 Feb 1998 22:42:56 GMT Organization: Ireland On-Line Lines: 9 Message-ID: <34de2d2c.2353041@news.iol.ie> Reply-To: coupers@iol.ie NNTP-Posting-Host: dialup-001.mullingar.iol.ie X-Newsreader: Forte Free Agent 1.11/16.235 Hi Does anyone know of a program for comparing different version of a text report and highlighting differences? I saw something years ago but can't remeber where. Thanks David Couper From owner-software@net.bio.net Tue Feb 10 22:00:00 1998 Date: Wed, 11 Feb 1998 21:43:16 +0100 From: gerard@xray.bmc.uu.se (Gerard Kleywegt) Newsgroups: sci.med.informatics,comp.ai,comp.ia.nat-lang,bionet.software Subject: Re: 2nd CFP: AAAI-98 Wkshp on Knowledge Sharing Across Bio and Med KB Systems Message-ID: References: <34E0BBDC.3F4D@glaxowellcome.com> Organization: SBNet - Uppsala University X-Newsreader: Value-Added NewsWatcher 2.1d3+ NNTP-Posting-Host: nostromo.bmc.uu.se Lines: 20 Path: biosci!agate!newsgate.duke.edu!nntprelay.mathworks.com!fci-se!fci!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!130.238.7.13.MISMATCH!newsfeed.uu.se!nostromo.bmc.uu.se!user In article <34E0BBDC.3F4D@glaxowellcome.com>, ghm48805@glaxowellcome.com wrote: >The amount of biological and medical information is growing at an >exponential rate and overwhelming researchers and clinicians. Various >groups have applied the technology of knowledge base systems to help in >the effective utilization of available information. These systems have >been used for applications in information retrieval, natural language >processing, database integration, machine earning, data mining, and *************** >decision-making. "machine earning" - you mean computers that wash cars at trafic lights ? or is this about automatic spam generators of the 'get rich quick' ilk ??? --cd ---------------------------------------------------------- Gerard Kleywegt mailto:gerard@xray.bmc.uu.se http://alpha2.bmc.uu.se/~gerard/ From owner-software@net.bio.net Tue Feb 10 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!su-news-feed4.bbnplanet.com!news.bbnplanet.com!zeus!not-for-mail From: "Joe Wang" Newsgroups: bionet.software Subject: A test Lines: 609 MIME-Version: 1.0 Content-Type: multipart/related; type="multipart/alternative"; boundary="----=_NextPart_000_0215_01BD365F.41538EB0" X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Message-ID: <34e12388.0@news.asante.com> Date: Wed, 11 Feb 1998 04:06:19 GMT NNTP-Posting-Host: maxima.asante.com NNTP-Posting-Date: Tue, 10 Feb 1998 20:06:19 PST This is a multi-part message in MIME format. ------=_NextPart_000_0215_01BD365F.41538EB0 Content-Type: multipart/alternative; boundary="----=_NextPart_001_0216_01BD365F.41538EB0" ------=_NextPart_001_0216_01BD365F.41538EB0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable TIME 08:05 PM 02-10-1998 ------=_NextPart_001_0216_01BD365F.41538EB0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

TIME 08:05 PM = 02-10-1998
 
3D""
------=_NextPart_001_0216_01BD365F.41538EB0-- ------=_NextPart_000_0215_01BD365F.41538EB0 Content-Type: image/gif Content-Transfer-Encoding: base64 Content-ID: <020c01bd36a2$4f4d74c0$ccfa6cc0@mis-joe.asante.com> R0lGODlhKgIoAIMAAQAAAICAgMDAwP///wAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAACH/C05FVFNDQVBFMi4wAwEAAAAh+QQAAQD/ACwAAAAAKgIoAAME/lDISau9OOvNu/9gKI5k aZ5oqq5s675wLM90bd94ru9876sBSWBILBqPyKRyyWw6n9CodEqtWq/YrHbL7Xq/4DAWIBSbz+i0 es1uu9/weFsACAqI9XxAz9/7+4B/goGEg4aFiIeKiYyLjo2Qj5KRlJOWlZiXmpmcm56doJ+ioZBC ZHejqaSqrKuurbCvsrG0s7a1uLe6nxN1ZXsAwcLDxMXGx8jJysvMzc7P0NHS09TV1tfY2drb3N3e 380Ue2V6fuZ150Po6+rt6e/s8O7x9PP28vj1+ff6/fz/+wL6EwhwoMGCCAkqPLgwIcOHDiM2nAiR osSK/U5J8IUKWBBf/iA/iqQzMiTJkyZTllyJkqXKljBfynRJM2bNmTZz4tx5s6dOnzx/Cg1KFKjR oUeLIl2qtGnSp0xvarxzqh24q1izat3KtavXr2DDisVKgSMejBfTWlyLlq3atnDfynVLN27duXbz 4t17ty/GqeNQ6YlK2GlhqIYTI158uLFix4wfS45MGbLlyZcrN51qVt3Yz6BDix5NurTp01rFVRXk l6/e1rBfy3ZNO3bt2bZz4959uzc8znbOah6euTjm48SRG0/OfLlz5dCbR3/uEvDqPKiza9/Ovbv3 7+CB/wrmm7fu8ujPqzfPPn379e7jwxdonZwf6vin65fOP3///f4F/gjggP8VOJR4HYWn4IIMNujg gwuqZt97FMpX4XwXZmjhhhhyqGGHfiEonIAGEkjiiSamWOKKKLKoYouO1ScYMBDWaOONOOaoozNl BeeZh0CC+OGQQRIpZJFIHqmkQTJa5eKTML4oJZRTRknllVZmuZOInu3o5ZdghikmaRLOaOSZSaK5 ZJpsrummmnBexKVHWmJZ5Z125lnnnnjyqeeWZVo15qCEFmrooc/0OF6cb7bJ6KOORtropJCGGKgg fmba56Z/dqqpp5x+etmciJZq6qmo6nhpOZW2KqmrlL4qa6y0wklqqLiCqquoufK6a6/ANvlHqsQW a+yxoyma4A/MYDbr7LPQRivttNS+EJg61War7bbcduvtt952Jse45JZr7rnopqvuunNQ9Qu78MYr 77z01mvvvUecRFUu/O7ib78A/ytwwAQPbHDBCB8MyL4KJ+xwwxA/LHHEFE9sccW7AAAh+QQAKAD/ ACwHAAcAHAIaAAME/jAEIOms+GrLc99eCI5fKZrkqaYs6q5vC89yHd80buf87uvAXvAnLBKPnMGA ImA6A03oM0qdWqXYavaq7XK/27BXDB6by2iy+rxOs9/ueHsOp8vr+Lvezs/3935VAxMAhYaHiImK i4yNjo+QkZKTlJWWl5iZmpucnZ6foKGio49GQ6emqUiqqKuurbCssq+zsbS3trm1uzZKgL9/wYHA w8LE