From owner-software@net.bio.net Sun Jan 01 22:00:00 1995 Path: biosci!newshost.lanl.gov!news.ttu.edu!seas.smu.edu!convex!insosf1.infonet.net!solaris.cc.vt.edu!news.alpha.net!uwm.edu!lll-winken.llnl.gov!overload.lbl.gov!agate!library.ucla.edu!psgrain!nntp.cs.ubc.ca!unixg.ubc.ca!worm.biochem.ubc.ca!user From: mleroux@unixg.ubc.ca (Michel Leroux) Newsgroups: bionet.software Subject: Re: PC Sequence Analysis Date: 31 Dec 1994 22:50:51 GMT Organization: Dept. of Biochemistry, U.B.C Lines: 13 Message-ID: References: NNTP-Posting-Host: worm.biochem.ubc.ca In article , SINGLETARYGW@phibred.com wrote: > Can anyone recommend PC software for nt/pep sequence alignment, database > searching (i.e., CD-ROM) and local analysis/manipulation. I've used DNASIS > before and liked it, but in setting up a new machine at a new location, I > would like to know if better choices exist. Thanks! > > GWS > Email: singletarygw@phibred.com PCGENE is probably the best one for the PC. I'm not sure where you can get it from, though. From owner-software@net.bio.net Sun Jan 01 22:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!sunsite.doc.ic.ac.uk!agate!howland.reston.ans.net!pipex!uunet!newsflash.concordia.ca!CC.UMontreal.CA!megasun.BCH.UMontreal.CA!tim From: tim@megasun.BCH.UMontreal.CA (Tim Littlejohn) Subject: Re: ABI373-like Software Message-ID: Sender: news@cc.umontreal.ca (Administration de Cnews) Organization: Universite de Montreal References: <3dmta2$h0g@msunews.cl.msu.edu> <3361@alsys1.aecom.yu.edu> <1994Dec29.223553.9975@galileo.cc.rochester.edu> Date: Sat, 31 Dec 1994 23:43:14 GMT Lines: 31 In article <1994Dec29.223553.9975@galileo.cc.rochester.edu> ajp2o@crocus.medicine.rochester.edu (Anthony J. Persechini) writes: > With reference to software able to display and manipulate ABI trace files, > there were two Xwindows (Unix) programs floating around the net for a while: > Ted (Trace Editor) and Phred(?). ted is part of the Staden package. >I have been unable to find either recently. If someone out there knows how to >get a hold of these programs, I am sure it would be of general interest. More information about the Staden package can be obtained from: URL: gopher://megasun.bch.umontreal.ca:70/11/CMB/Staden or at the newsgroup: bionet.software.staden Tim -- ============================================================================== Tim Littlejohn E-mail: tim@bch.umontreal.ca Snail Mail: Departement de biochimie Phone: (514) 343-6111, x5149 Universite de Montreal Fax: (514) 343-2210 C.P. 6128, Centre-ville Montreal (Quebec), H3C 3J7 CANADA ============================================================================== From owner-software@net.bio.net Sun Jan 01 22:00:00 1995 Newsgroups: bionet.software Path: biosci!newshost.lanl.gov!news.ttu.edu!seas.smu.edu!convex!insosf1.infonet.net!news-feed-1.peachnet.edu!gatech!swrinde!pipex!uunet!newsflash.concordia.ca!CC.UMontreal.CA!megasun.BCH.UMontreal.CA!tim From: tim@megasun.BCH.UMontreal.CA (Tim Littlejohn) Subject: Re: GDE and Solaris 2.4 Message-ID: Sender: news@cc.umontreal.ca (Administration de Cnews) Organization: Universite de Montreal References: Date: Sat, 31 Dec 1994 23:57:41 GMT Lines: 26 In article COISSAC@OXYDASE.CGM.CNRS-GIF.FR (Eric COISSAC) writes: > > I have just install Solaris 2.4 on my Sun, and now I have some problem >to compile program like GDE on it. I look for some one who have binarie of >GDE for sun solaris 2, or modified source. I maintain an archive of GDE source code and some executables (SunOS, DEC and Linux). If anyone would like to contribute a collection of Solaris binaries (GDE and associated programs [e.g. clustal]) I would be happy to distribute them through this site: URL: gopher://megasun.bch.umontreal.ca:70/11/GDE Tim -- ============================================================================== Tim Littlejohn E-mail: tim@bch.umontreal.ca Snail Mail: Departement de biochimie Phone: (514) 343-6111, x5149 Universite de Montreal Fax: (514) 343-2210 C.P. 6128, Centre-ville Montreal (Quebec), H3C 3J7 CANADA ============================================================================== From owner-software@net.bio.net Sun Jan 01 22:00:00 1995 Newsgroups: bionet.software From: Duncan@genesys.demon.co.uk (Duncan Clark) Path: biosci!newshost.lanl.gov!news.ttu.edu!seas.smu.edu!convex!insosf1.infonet.net!news-feed-1.peachnet.edu!gatech!howland.reston.ans.net!pipex!demon!genesys.demon.co.uk!Duncan Subject: PC Sequence analysis Distribution: world Organization: GeneSys Ltd. Reply-To: Duncan@genesys.demon.co.uk X-Newsreader: Newswin Alpha 0.6 Lines: 18 X-Posting-Host: genesys.demon.co.uk Date: Sun, 1 Jan 1995 10:23:30 +0000 Message-ID: <476199120wnr@genesys.demon.co.uk> Sender: usenet@demon.co.uk Hi Folks, Does anyone know of a package that would help me do do the following: 1. Alignment of aa sequences 2. Having aligned sequences, use that aa alignment to put back in the DNA sequence. Sounds simple but a real sod to do manually for 4 x 2500bp sequences when many gaps are involved. I did the original aa alignment with Clustal5 and then spent 3+ hours for the rest. Nice New Year! Duncan ----------------------------------------------------------------------------- My mind's made up. Don't confuse me with the facts! From owner-software@net.bio.net Sun Jan 01 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!ix.netcom.com!netnews From: kitani@ix.netcom.com (Ken Itani) Newsgroups: bionet.software,comp.ai.neural-nets Subject: Re: Commercial Neural Network Software Date: 2 Jan 1995 21:06:36 GMT Organization: Netcom Lines: 63 Distribution: world Message-ID: <3e9pss$ocl@ixnews3.ix.netcom.com> References: <3deldc$i3s@mserv1.dl.ac.uk> <3dnjp5$cs4@riscsm.scripps.edu> NNTP-Posting-Host: ix-pit2-08.ix.netcom.com Xref: biosci bionet.software:10523 comp.ai.neural-nets:12112 In <3dnjp5$cs4@riscsm.scripps.edu> misrael@scripps.edu (Mark Israel) writes: > >In article <3deldc$i3s@mserv1.dl.ac.uk>, vanhannen@cl.nioo.nl (Erik van Hannen) writes: > >> Hi to everybody, >> >> I'm a PhD student in microbial ecology from the Netherlands. One of my jobs >> is to identify flagellates with the use of flow cytometry. I want to use a >> neural network to analyse my data. Up till now I've been using BrainMaker to >> do the job. But I want to buy a Windows Neural Network program. Can somebody >> give me some names of programs or comapanies who sell it? > > (I've cross-posted this from bionet.software to comp.ai.neural-nets; >someone there may be able to give you more specific advice.) > > BrainMaker *does* run under MicroSoft Windows; so do many other >Neural Network programs. There is a list of them in the >comp.ai.neural-nets FAQ file. I have e-mailed you the relevant >portion. Others can obtain it by anonymous ftp: > > ftp rtfm.mit.edu > anonymous > (your e-mail address) > cd /pub/usenet/comp.ai.neural-nets > get FAQ_in_comp.ai.neural-nets_--_monthly_posting > quit > >or on the World Wide Web: > > Mosaic http://wwwipd.ira.uka.de/Tichy/neural-net-faq.html > >-- >misrael@scripps.edu Mark Israel > Mark, I think we may have en EXTREMELY PRECISE neural circuit modeling and simulation tool, which is very new and is NOT BASED ON CONNECTIONIST paradigm. I fyou are interested, send me your postal mail address, and I'll send you a complete packet of information including an example of a 4-cell neural module (which in the demo diskette), that alone may outperform the entire network of a Connectionist paradigm-based tool. Regards, --Ken --Ken -- ====================================================================== Ken Itani A frontiersman gets many more arrows shot ITANIS International, Inc. at than the settlers who follow him. His 1737 Holly Lane only allies are his wits, tenacity, perce- Pittsburgh, PA 15216-1151 verance, and diligence, which alone would U.S.A. help him survive in the presence of const- Voice: +412-344-4553 ant and relentless challenges, seemingly FAX: +412-344-3541 overwheling odds against him, incessant Order: 1-800-ITANIS-1 threats of a disaster and creeping despair. email: kitani@ix.netcom.com ====================================================================== From owner-software@net.bio.net Sun Jan 01 22:00:00 1995 Path: biosci!HARVARD.EDU!greenes From: greenes@HARVARD.EDU (Robert A. Greenes) Newsgroups: bionet.software Subject: Harvard-MIT-NEMC Postdoc fellowships in Medical Informatics Date: 2 Jan 1995 09:14:35 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 85 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net *** Postdoctoral Fellowships Available for AY 1994 *** HARVARD, MIT, and TUFTS/NEW ENGLAND MEDICAL CENTER COMBINED RESEARCH TRAINING PROGRAM IN MEDICAL INFORMATICS Openings are available for qualified applicants for the Harvard Medical School, MIT, Tufts/New England Medical Center combined training program in medical informatics, for July, 1994 or later. Research training fellowships are available at three participating laboratories: o Decision Systems Group, Brigham and Women's Hospital (under the direction of Robert A. Greenes, M.D., Ph.D.), emphasizing clinical decision making, medical educational strategies, clinical guidelines, clinical record keeping, medical knowledge representation and query, radiologic image management, and collabo- rative architectures for network-based application development. See also WWW page: http://dsg.harvard.edu/ o Laboratory of Computer Science, Massachusetts General Hospital (under the direction of G. Octo Barnett, M.D.), emphasizing clinical decision making, medical student education, student/physician workstation design, problem-based knowledge access, ambulatory computer-based medical record systems, and implementation/evaluation of guidelines o Division of Clinical Decision Making, NEMC (under the direction of Stephan G. Pauker, M.D.), emphasizing clinical decision making, knowledge representation, and guidelines and outcome evaluation Fellowships involve in-depth experience in the ongoing research programs of the participating laboratories, with emphasis on assumption of project responsibility, leading to publication, presentation, and independent funding. Our goal is to train individuals who will be well-equipped to be leaders of medical informatics programs of their own, or to bring these skills to their clinical specialties. Research fellows typically take 1-2 courses per term in addition to their project work. Those wishing a degree may concurrently apply for admission to the masters or doctoral programs in Medical Computer Science at the MIT Department of Electrical Engineering/ Computer Science, or in Health Decision Science at Harvard School of Public Health, Department of Health Policy and Management. The combined training program offers a wide range of opportunities for education, research, and collegial interaction among the training sites. A large variety of course offerings at Harvard, MIT, and Tufts, many seminars, journal clubs, and other opportuities for exchange of information provide all trainees with opportunities to learn about the variety of work occurring at the various laboratories and in the affiliated institutions, as well as in the larger field of medical informatics. A number of associated faculty participate in the program through the research activities of each of the training sites. In addition to the research programs of the participating laboratories, we encourage the fellows to develop projects that may involve unique collaborative relationships. Applicants must be physicians or doctorates in other health care or biomedical fields or in computer science. Physcians will usually have at least one year and preferably three years of residency training prior to beginning of fellowship. Prior computer experience is strongly preferred. Fellowship support includes a postdoctoral stipend, health insurance, tuition, and travel funds. FELLOWSHIP SUPPORT IS AVAILABLE ONLY TO U.S. CITIZENS OR PERMANENT RESIDENTS. Others may apply, but only if they have independent external sources of support. For more information, contact the program office: Medical Informatics Training Program ATTN: Robert A. Greenes, MD, PhD Decision Systems Group, Brigham and Women's Hospital 75 Francis Street, Boston, MA 02115 (617) 732-6281 FAX: (617) 732-6317 email: greenes@harvard.edu or the individual training program component directors via email at: Barnett: obarnett@hstbme.mit.edu Greenes: greenes@harvard.edu Pauker: sgp@cor.cdm.nemc.org From owner-software@net.bio.net Sun Jan 01 22:00:00 1995 Newsgroups: bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!bloom-beacon.mit.edu!uhog.mit.edu!rutgers!princeton!hedgehog.Princeton.EDU!news From: Fredrik Hans Oskar Osterberg Subject: X-ray Absorbtion Corrections Content-Type: TEXT/PLAIN; charset=US-ASCII Message-ID: Originator: news@hedgehog.Princeton.EDU Sender: news@Princeton.EDU (USENET News System) Nntp-Posting-Host: bigbro.princeton.edu Organization: Princeton University Mime-Version: 1.0 Date: Mon, 2 Jan 1995 15:33:03 GMT Lines: 17 Dear Bionet Readers, I am aware that several programs have been written that will correct for absorbtion effects in crystallographic data. However, I wonder if anyone knows which is the best software for this, and where it can be found. Fredrik Osterberg ___________________________________________________________________________ Address:Physics Dept. Jadwin Hall Tel: 1-(609)258 4359 Princeton University Fax: 1-(609)285 1124 Princeton, NJ 08544, U.S.A. Email: fredrik@bigbro.princeton.edu ___________________________________________________________________________ From owner-software@net.bio.net Mon Jan 02 22:00:00 1995 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!news.cs.indiana.edu!iedsp@ctf1-5.agt.gmeds.com From: iedsp@ctf1-5.agt.gmeds.com (David S. Pesetsky 230-6088 AGT) Subject: Looking for software... Message-ID: <9501031554.AA33972@ctf1-5.agt.gmeds.com> Sender: root@news.cs.indiana.edu (Operator) Organization: Computer Science, Indiana University Date: Tue, 3 Jan 1995 10:54:37 -0500 Lines: 15 I'm looking for some freeware or shareware to help with cartoons. I'd like to be able to create a cartoon character and quickly show it in different positions, i.e. running, crouching over, from the back, etc... Annimation is not needed. I also am looking for some morphing software. Note: I'm on an IBM RISC6000 running AIX Please respond via e-mail since I don't subscribe to USENET :( iedsp@agt.gmeds.com Thanks! Dave From owner-software@net.bio.net Mon Jan 02 22:00:00 1995 Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!news.cc.utah.edu!kr5205 From: kr5205@u.cc.utah.edu (Kerry Rowe) Newsgroups: bionet.software Subject: REQUEST: lab instrument integration/interfacing systems Date: 3 Jan 1995 22:43:07 GMT Organization: University of Utah Lines: 15 Message-ID: <3ecjtr$lj1@news.cc.utah.edu> NNTP-Posting-Host: u.cc.utah.edu I am interested in any available info on systems (hardware/software) for tracking samples (perhaps using barcodes) and gathering data as samples traverse a series of laboratory systems. Any pointers to commercial or other tools would be appreciated. Thanks in advance. Steve Bayer Myriad Genetics, Inc. 390 Wakara Way, Salt Lake City, UT 84108 (801) 584-3642 (801) 584-3640 - fax bayer@myriad.com From owner-software@net.bio.net Mon Jan 02 22:00:00 1995 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: worm@dsa.mpi-muelheim.mpg.de (Karl-Heinz Worm) Newsgroups: bionet.software Subject: Re: FarFetch on Network Date: 3 Jan 1995 14:59:45 -0000 Lines: 24 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3ebop1$6cc@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk In bionet.software Msg # 7923 K Y Hwa wrote >Dear Netters: > >I am looking for a Mac-program called FarFetch. Any one has idea where I >can download this program? Thank you very much. KY via FTP from genome.wi.mit.edu:/distribution/software/blast_client/FarFetch__1.1.hqx --------------------------------------------------------------------------- Karl Worm # Max-Planck-Institut f. Strahlenchemie # Stiftstrasse 34-36 # Tel.: 0208-3063673 45470 Muelheim an der Ruhr # Fax: 0208-3063951 Germany # e-mail:worm@dsa.mpi-muelheim.mpg.de --------------------------------------------------------------------------- From owner-software@net.bio.net Mon Jan 02 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!gatech!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!caen!usenet.coe.montana.edu!Msu.oscs.montana.edu!ueybnjb From: ueybnjb@Msu.oscs.montana.edu Newsgroups: bionet.software Subject: Address info. for author of Biosys (Dr. Swofford)? Date: Tue, 03 Jan 1995 15:23:35 Organization: Montana State University Lines: 4 Distribution: world Message-ID: <00989EA6.70D3ACE0@Msu.oscs.montana.edu> Reply-To: ueybnjb@Msu.oscs.montana.edu NNTP-Posting-Host: trex.oscs.montana.edu I need to redimension parameters of Biosys program. I cannot find the current email address or phone # of the author, David L. Swofford, who can help me with this problem. If you can tell me, I will be most grateful! I am: Joe Bunnell (406) 994-4212 UEYBNJB@msu.oscs.montana.edu From owner-software@net.bio.net Tue Jan 03 22:00:00 1995 Path: biosci!ARGO.URV.ES!pujadas From: pujadas@ARGO.URV.ES (Gerard Pujadas BQ 2253) Newsgroups: bionet.software Subject: Mac Mollecular Modelling Soft Date: 3 Jan 1995 23:57:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <9501040755.AA35132@quimica.urv.es> Hi, my name is Gerard Pujadas and I am looking for a cheap Mollecular Modelling program for Macintosh. Does anybody know a program of this characte- ristics? Thanks and good year to all the neters. Gerard Pujadas Dept. Bioquimica i Biotecnologia Universitat Rovira i Virgili Plac,a Imperial Tarraco 1 43005 Tarragona (CATALONIA) Europe. e-mails: pujadas@quimica.urv.es utabbt01@cadi.cesca.es telf: (34 77) 55 95 65  From owner-software@net.bio.net Tue Jan 03 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!uunet!psinntp!wanchai.hk.super.net!hk.super.net!johnnycw From: johnnycw@hk.super.net (Mr Wah Chan) Newsgroups: bionet.software Subject: US Contact: American Management System, Systemetic Inc. Date: 4 Jan 1995 22:42:46 GMT Organization: Hong Kong Supernet Lines: 21 Message-ID: <3ef896$55e@hk.super.net> NNTP-Posting-Host: 202.14.67.232 X-Newsreader: TIN [version 1.2 PL2] Anyone hears about the following companies: American Management System Systemetic Inc. Both companies specialize on Telephone Billing Systems. We need to know their US contact and also their Rep Office in HK or SE Asia. Suggestion on how to find such info are also welcomed. (e.g., sites where I can find out the address and tel# of any US companies, etc.) -- Johnny *************************** Johnny Chan ********************************** Internet Address: johnnycw@hk.super.net Jesus is my savior, and He can be yours, too. !!!!!!! *************************************************************************** From owner-software@net.bio.net Tue Jan 03 22:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!uknet!comlab.ox.ac.uk!oxuniv!ayoung From: ayoung@vax.oxford.ac.uk (Geordie +1865 740 011) Newsgroups: bionet.molbio.genome-program,bionet.software Subject: version 1.2 of GAS now available Message-ID: <1995Jan4.210838.28261@oxvaxd> Date: 4 Jan 95 21:08:38 GMT Organization: Oxford University VAX 6620 Lines: 33 Xref: biosci bionet.molbio.genome-program:1096 bionet.software:10536 The GAS program has now been updated to Version 1.2, which is available via anonymous ftp from well.ox.ac.uk in directory pub/genetics/gas. For users new to this package, it provides facilities for reading, writing, sectioning and performing statistical analyses on phenotypic and genotypic data. It has been developed within the department of medicine at Oxford University and is available via ftp as freeware. The main additions to the previous version include: * full use of extended memory on IBM 486/Pentium PCs * association tests for marker/candidate alleles and diseases * extended categories of select(), including marker alleles * maximum-likelihood estimates for sib-pair IBD In response to requests the section of the manual devoted to the select() command has been enlarged with further examples. A minor bug gas been corrected in 1.1 sibstate(). This was giving too low p-values and has been corrected in version 1.2. No other bugs were reported. Directions for unpacking the program and documentation are in the file `README' available via anonymous ftp from directory pub/genetics/gas at well.ox.ac.uk -- ------------------------------------------------------------------------------- ___ / \ / | / Alan Young @ uk.ac.ox.vax /____/ / ___ __ |___/ / / / / | / | / "The bigger they are, / \_/\__\__/|_/ /_________/ the harder they fall on you." From owner-software@net.bio.net Tue Jan 03 22:00:00 1995 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!world!chi From: chi@world.std.com (Cambridge Healthtech Institute) Subject: Computer-Aided Drug Development Meeting Message-ID: Organization: The World Public Access UNIX, Brookline, MA X-Newsreader: TIN [version 1.2 PL2] Date: Wed, 4 Jan 1995 03:17:09 GMT Lines: 19 Cambridge Healthtech Institute is organizing programs on Computer Aided Drug Development. This conference is to be held April 12-13, 1995 in San Francisco, California. For further program information, conference registration materials, information on presenting posters, contact Cambridge Healthtech Institute, chi@world.std.com. Inquiries are welcome. *********************************************************************** *>>>>>>>>>>>> Cambridge Healthtech Institute <<<<<<<<<<<<<* *>>>>> 1000 Winter Street, Suite 3700 <<<<<* *~~~~~~~~~~~~~~~~~ Waltham, MA 02154 ~~~~~~~~~~~~~~~~~* *tel: 617.487.7989 fax: 617.487.7937* *e-mail: chi@world.std.com ++++++++ ftp: ftp.std.com: /pub/chi* *>>>>>>>>>>>>World Wide Web: http://id.wing.net/~chi/homepg.html<<<<<<* *********************************************************************** From owner-software@net.bio.net Tue Jan 03 22:00:00 1995 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!Germany.EU.net!news.dfn.de!zeus.rbi.informatik.uni-frankfurt.de!terra.wiwi.uni-frankfurt.de!news.th-darmstadt.de!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: plasmid inventory control Date: 4 Jan 1995 14:56:24 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 25 Distribution: world Message-ID: <3eecuo$382h@sat.ipp-garching.mpg.de> References: <3ecmoj$nf6@gazette.bcm.tmc.edu> NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] Paula Burch (pburch@roc.mbcr.bcm.tmc.edu) wrote: > One of our users wants a program that can keep track of the maps > of a 100 or so plasmids and has the ability to draw the plasmid, > name its parts, and give a reference if appropriate. > She's interested in a PC program, if possible, but if there's a > solution to her needs involving a UNIX program, we can install it > for her on our system, and we're also interested in Mac solutions. > We have access to the GCG package and the IG Suite. The GCG program PLASMIDMAP is able to draw plasmids. If the sequence is available, PLASMIDMAP input can be generated from MAP; otherwise, you have to fiddle with an ASCII editor (it's not too difficult when you have got used to it). PLASMIDMAP can add a few lines of text to the plasmid drawing, if this is sufficient for the reference. AFAIK there is no free plasmid drawing program for Microsoft Windows. I'm not sure about programs for DOS. --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "Science is the game you play with God to find out what His rules are." */ From owner-software@net.bio.net Tue Jan 03 22:00:00 1995 Path: biosci!lhc!darwin.sura.net!maze.dpo.uab.edu!uabcvsr!txpljfg From: txpljfg@uabcvsr.seas.ucla.edu () Newsgroups: bionet.software Subject: Re: plasmid inventory control Date: 4 Jan 1995 17:14:57 GMT Organization: University of Alabama at Birmingham Lines: 43 Message-ID: <3eel2h$h60@maze.dpo.uab.edu> NNTP-Posting-Host: uabcvsr.cvsr.uab.edu X-Newsreader: TIN [version 1.2 PL2] There is a program called CLONE from Scientific and Educational Software that is superb for drawing and storing plasmid maps. It runs under DOS and is relatively inexpensive > Paula Burch (pburch@roc.mbcr.bcm.tmc.edu) wrote: > > One of our users wants a program that can keep track of the maps > > of a 100 or so plasmids and has the ability to draw the plasmid, > > name its parts, and give a reference if appropriate. > > She's interested in a PC program, if possible, but if there's a > > solution to her needs involving a UNIX program, we can install it > > for her on our system, and we're also interested in Mac solutions. > > We have access to the GCG package and the IG Suite. > The GCG program PLASMIDMAP is able to draw plasmids. If the sequence > is available, PLASMIDMAP input can be generated from MAP; otherwise, > you have to fiddle with an ASCII editor (it's not too difficult when > you have got used to it). PLASMIDMAP can add a few lines of text to > the plasmid drawing, if this is sufficient for the reference. > AFAIK there is no free plasmid drawing program for Microsoft Windows. > I'm not sure about programs for DOS. > --Cornelius. > -- 4~> /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ 4~4~> /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ 4~> /* "Science is the game you play with God to find out what His rules are." */ -- ============================================================================== James F. George, Ph.D. "Back off man, I'm a scientist" Department of Surgery --Bill Murray University of Alabama at Birmingham 205-934-4261 voice txpljfg@uabcvsr.cvsr.uab.edu =============================================================================== From owner-software@net.bio.net Tue Jan 03 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!news.starnet.net!wupost!newspump.wustl.edu!bcm!roc.mbcr.bcm.tmc.edu!pburch From: pburch@roc.mbcr.bcm.tmc.edu (Paula Burch) Newsgroups: bionet.software Subject: plasmid inventory control Date: 3 Jan 1995 23:31:31 GMT Organization: Baylor College of Medicine, Houston, Tx Lines: 20 Distribution: world Message-ID: <3ecmoj$nf6@gazette.bcm.tmc.edu> NNTP-Posting-Host: roc.mbcr.bcm.tmc.edu One of our users wants a program that can keep track of the maps of a 100 or so plasmids and has the ability to draw the plasmid, name its parts, and give a reference if appropriate. She points out that while programs such as MacVector will do some of this, they cost in the thousands of dollars and represent rather extreme overkill for what she wants to do. She says there's got to be something simpler that will do what she needs. Any suggestions? She's interested in a PC program, if possible, but if there's a solution to her needs involving a UNIX program, we can install it for her on our system, and we're also interested in Mac solutions. We have access to the GCG package and the IG Suite. ________________________________________________________________________ Paula E. Burch, Ph.D. Molecular Biology Computational Resource Baylor College of Medicine phone: (713)798-6023 fax: (713)798-4279 Houston, Texas 77030 internet: pburch@bcm.tmc.edu http://condor.bcm.tmc.edu/pburch.html From owner-software@net.bio.net Tue Jan 03 22:00:00 1995 Newsgroups: bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!pipex!uunet!EU.net!Austria.EU.net!newsfeed.ACO.net!edvz.sbg.ac.at!wst!floeckn From: floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) Subject: Structural protein similarity program Message-ID: Lines: 12 Sender: floeckn@wst (Floeckner Hannes) Reply-To: floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) Organization: University of Salzburg / Austria Date: Wed, 4 Jan 1995 12:54:34 GMT Hi! I'm looking for public domain programs for structure-structure alignments and for the identification of structural similarities in protein folds. The program should run on either SGI or Dec-Alpha (in the worst case on MS-DOS PC's). Anyone who knows a program to do structure-strucutre alignment? Thanx Hannes From owner-software@net.bio.net Tue Jan 03 22:00:00 1995 Path: biosci!newshost.lanl.gov!news.ttu.edu!seas.smu.edu!convex!insosf1.infonet.net!news-feed-1.peachnet.edu!news.duke.edu!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: st23646@ggr.co.uk Newsgroups: bionet.software Subject: cDNA extraction from databases Date: 4 Jan 1995 16:25:14 -0000 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3eei5a$da2@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk I seem to remember some time ago I saw some freeware which allowed you to extract relevant information from EMBL or Genbank database entry feature tables. I would like to be able to pull out full length cDNAs from a collection of database entries and don't want to have to examine every feature table by hand to find where the exons are ! Anything that does this sort of operation would be useful. Can anybody please help ? Regards, Steve Taylor, Glaxo R & D, England From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!psuvax1!rutgers!utcsri!yonge.cs.toronto.edu!neuron.ai.toronto.edu!ai.toronto.edu!steeg Newsgroups: bionet.software,bionet.molbio.proteins,bionet.molec-model From: steeg@cs.toronto.edu ("Evan W. Steeg") Subject: Pictures/coordinates for states in protein folding Message-ID: <95Jan4.201837edt.280@neuron.ai.toronto.edu> Originator: root@yonge.cs.toronto.edu Nntp-Posting-Host: yonge.cs.toronto.edu Organization: CS Lab, University of Toronto Distribution: bionet Date: 5 Jan 95 01:19:19 GMT Lines: 37 Xref: biosci bionet.software:10540 bionet.molbio.proteins:3368 bionet.molec-model:220 A friend of mine would like some pictures of a protein in several different states of folding/unfolding. She'd really prefer Cytochrome C, but other proteins would suffice. Otherwise, her needs are very flexible: -- Intermediate states may be observed (NMR, etc.) or modelled (according to some accepted classical/qm simulation model). -- Pictures may be space-filling, or ribbon diagrams, or etc. -- Pictures in any unix-friendly format (gif, tiff, ppm, etc.) In addition to or in lieu of graphics, perhaps there is a database of partially-folded structures somewhere, akin to the brookhaven pdb of folded structure coordinate files? I'm curious about this myself. Last but not least, can anyone recommend offhand a particularly good paper on some theoretical or empirical aspects of folding that features a sequence of pictures as described above (especially of Cyt C!) ? Thanks for any pictures, pointers, or references! If I discover anything especially interesting, I'd be glad to summarize and repost. Regards, Evan Evan W. Steeg (416) 978-5182 steeg@ai.toronto.edu Dept of Computer Science steeg@t13.lanl.gov University of Toronto, Toronto, Canada M5S 1A4 FAX: (416) 978-1455 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- "We tend to scoff at the beliefs of the ancients. But we can't scoff at them personally, to their faces, and this is what annoys me." - Jack Handey =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!umn.edu!lenti.med.umn.edu!rogene From: rogene@lenti.med.umn.edu (Rogene M. Eichler West) Subject: Lifeforms or equiv Message-ID: Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: lenti.med.umn.edu Organization: University of Minnesota Date: Thu, 5 Jan 1995 06:29:58 GMT Lines: 16 Has anyone had experience using the software "Lifeforms", or does anyone know of other Macintosh software for rendering human forms? Models/animations are needed for the demonstration of forces during strength training. Any info appreciated. Please reply email. rogene@lenti.med.umn.edu Thanks! -Rogene From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!CLASS.ORG!ljenkins From: ljenkins@CLASS.ORG Newsgroups: bionet.software Subject: (none) Date: 4 Jan 1995 11:11:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: Subscribe bio-software Laura Jenkins From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!uunet!newsflash.concordia.ca!canopus.cc.umanitoba.ca!tribune.usask.ca!quartz.ucs.ualberta.ca!unixg.ubc.ca!worm.biochem.ubc.ca!user From: mleroux@unixg.ubc.ca (Michel Leroux) Newsgroups: bionet.software Subject: Re: Structural protein similarity program Date: 5 Jan 1995 17:08:39 GMT Organization: Dept. of Biochemistry, U.B.C Lines: 51 Message-ID: References: NNTP-Posting-Host: worm.biochem.ubc.ca In article , floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) wrote: > Hi! > > I'm looking for public domain programs for structure-structure alignments and > for the identification of structural similarities in protein folds. The > program should run on either SGI or Dec-Alpha (in the worst case on > MS-DOS PC's). > > Anyone who knows a program to do structure-strucutre alignment? > > Thanx > Hannes Yes, I know of a program which may be just what you're looking for. It's called PHD, and its purpose is to predict the secondary structure of any given protein, and it also takes into account other similar (homologous) protein sequences. The more sequences it can compare to from the protein database, the better the prediction. They give a reference which claims the prediction is about 70% accurate. I have recently used it and found that the predicted GroEL secondary structure is VERY similar to the known secondary structure of this protein. It's available on any platform, and is very easy to use because it's a free e-mail service. All you need to do is send the following e-mail message: ------------------------------------------- To: PredictProtein@embl-heidelberg.de your name your address your e-mail address predict secondary structure # protein_name MAFGIHRTIPECV...(etc., your protein sequence) ------------------------------------------- You receive a confirmation of your request promptly, and then about half an hour later you get the secondary structure prediction. In your case, you'd have to compare the secondary structures manually, but this should serve your needs adequately. Michel Leroux mleroux@unixg.ubc.ca From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!gatech!newsxfer.itd.umich.edu!news.itd.umich.edu!prometheus.drda.umich.edu!cab From: Chris Beecher Newsgroups: bionet.software Subject: Scatchard Analysis Software Date: 5 Jan 1995 18:45:05 GMT Organization: University of Michgian Lines: 9 Distribution: world Message-ID: <3ehenh$fbr@lastactionhero.rs.itd.umich.edu> NNTP-Posting-Host: prometheus.drda.umich.edu X-UserAgent: Nuntius v1.1.1d24 X-XXMessage-ID: X-XXDate: Thu, 5 Jan 95 18:45:05 GMT I am looking for PC or Mac software that can do a Scatchard analysis for at least one-site ligand binding experiments. I am already familair with Ligand and it barely gets by, can anyone recommend something better without spending an arm and a leg? chris beecher Univ of Mich From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!pipex!uknet!comlab.ox.ac.uk!gjb From: gjb@bioch.ox.ac.uk (Geoff Barton) Subject: Re: Structural protein similarity program Message-ID: <1995Jan5.115608.303@geoff.bioch.ox.ac.uk> Originator: gjb@geoff.biop Organization: Laboratory of Molecular Biophysics, University of Oxford References: Date: Thu, 5 Jan 1995 11:56:08 GMT Lines: 33 In article , floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) writes: |> |> Hi! |> |> I'm looking for public domain programs for structure-structure alignments and |> for the identification of structural similarities in protein folds. The |> program should run on either SGI or Dec-Alpha (in the worst case on |> MS-DOS PC's). |> |> Anyone who knows a program to do structure-strucutre alignment? |> |> Thanx |> Hannes You could try STAMP (Russell and Barton, 1992, Proteins, 14, 309-323). Details of availability are available by anonymous ftp or WWW from the following addresses. Geoff. Barton ------------------------------------------------------------------------------- Geoffrey J. Barton Laboratory of Molecular Biophysics, University of Oxford Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K. email: gjb@bioch.ox.ac.uk Telephone: +44 1865 275368 Fax: +44 1865 510454 anonymous-ftp: geoff.biop.ox.ac.uk WWW: http://geoff.biop.ox.ac.uk ------------------------------------------------------------------------------- -- Geoff Barton From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!SILIBONE.CCHEM.BERKELEY.EDU!yang From: yang@SILIBONE.CCHEM.BERKELEY.EDU Newsgroups: bionet.software Subject: metal-binding sites Date: 4 Jan 1995 11:53:48 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <9501041949.AA28566@silibone.cchem.berkeley.edu> We are looking for programs which search backbone structures for metal-binding sites--specifically, we are interested in "designing" such sites in non-metallo enzymes in order to improve catalysis. Thanks in advance! =-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*- Priscilla L. Yang yang@paris.chem.yale.edu 909 Latimer Hall yang@silibone.cchem.berkeley.edu Berkeley, CA 94720 510 642-6026 =-*-=-*-=-*-=-*-=-*-=-*-= "You just go on your nerve." Frank O'Hara in "Personism: A Manifesto" =-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*-=-*- From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!newsserver.jvnc.net!cyanamid!ptag3.pt.cyanamid.com!bascombn From: bascombn@ptag3.pt.cyanamid.com Subject: Re: plasmid inventory control Message-ID: <1995Jan5.063148.1@ptag3.pt.cyanamid.com> Lines: 23 Sender: news@cyanamid.uucp Organization: AMERICAN CYANAMID AGRICULTURAL RESEACH CENTER References: <3ecmoj$nf6@gazette.bcm.tmc.edu> Date: Thu, 5 Jan 1995 11:31:48 GMT In article <3ecmoj$nf6@gazette.bcm.tmc.edu>, pburch@roc.mbcr.bcm.tmc.edu (Paula Burch) writes: > One of our users wants a program that can keep track of the maps > of a 100 or so plasmids and has the ability to draw the plasmid, > name its parts, and give a reference if appropriate. She points > out that while programs such as MacVector will do some of this, > they cost in the thousands of dollars and represent rather > extreme overkill for what she wants to do. She says there's > got to be something simpler that will do what she needs. > > Any suggestions? Scientific and Educational Software (P.O. Box 440, State Line, PA (717)597-5307 has a good PC package called "Clone" which allows you to do your cloning strategies, draw maps of the finished labeled plasmid and store it in a "database". The "Enhance" program allows you to make nice construction diagrams from all the pieces. The price isn't bad if I remember correctly, I think it was in the hundreds (as opposed to thousands) and the updates have been good. BTW, I do not work for them... Hope this helps. Newell Bascomb From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!news.starnet.net!wupost!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!fuw.edu.pl!news.nask.org.pl!ci.pwr.wroc.pl!prkom2.ch.pwr.wroc.pl!witek From: witek@kchk.ch.pwr.wroc.pl (Rafal Witek) Newsgroups: bionet.software Subject: help me Date: Thu, 5 Jan 1995 11:08:31 GMT Organization: PWr. I-30 Lines: 7 Message-ID: NNTP-Posting-Host: prkom2.ch.pwr.wroc.pl Where could I find any shareware of molecular biology , please send me mail messages at adress : witek@kchk.ch.pwr.wroc.pl From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: "Taylor Mr S" Newsgroups: bionet.software Subject: cDNA extracton from feature tables Date: 5 Jan 1995 09:54:55 -0000 Lines: 17 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3egflf$356@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk, bio-soft@dl.ac.uk I seem to remember some time ago I saw some freeware which allowed you to extract relevant information from EMBL or Genbank database entry feature tables. I would like to be able to pull out full length cDNAs from a collection of database entries and don't want to have to examine every feature table by hand to find where the exons are ! Anything that does this sort of operation would be useful. Can anybody please help ? Regards, Steve Taylor, Glaxo R & D, England From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!newsfeed.pitt.edu!uunet!newsflash.concordia.ca!canopus.cc.umanitoba.ca!bradbury!frist From: frist@cc.umanitoba.ca (Brian Fristensky) Newsgroups: bionet.software Subject: Re: cDNA extracton from feature tables Date: 5 Jan 1995 20:07:31 GMT Organization: The Univeristy of Manitoba. Lines: 58 Distribution: world Message-ID: <3ehji3$kat@canopus.cc.umanitoba.ca> References: <3egflf$356@mserv1.dl.ac.uk> Reply-To: frist@cc.umanitoba.ca NNTP-Posting-Host: bradbury.cc.umanitoba.ca In article 356@mserv1.dl.ac.uk, "Taylor Mr S" () writes: > I seem to remember some time ago I saw some freeware which allowed you > to extract relevant information from EMBL or Genbank database entry > feature tables. > See the XYLEM package which is available by anonymous FTP to directory 'psgendb' at ftp.cc.umanitoba.ca. The FEATURES program can extract any feature annotated in a GenBank entry, and even extract unannotated regions given user-supplied Feature expressions. A complete description of this process can be found in Fristensky, B. (1993) Feature expressions: creating and manipulating sequence datasets. Nucl. Acids Res. 21:5997-6003. > I would like to be able to pull out full length cDNAs from a collection of > database entries and don't want to have to examine every feature table > by hand to find where the exons are ! Anything that does > this sort of operation would be useful. > Steve Taylor, > Glaxo R & D, > England > It's not entirely clear what you mean here. cDNAs per se do not have introns to remove. Do you mean to say that you wish to extract a set of mRNAs from entries containing either cDNAs or genomic sequences? There is no feature key for cDNAs as such, but extracting using the 'mRNA' feature key will work where mRNA has been annoted in the GenBank entry. Unfortunately, it is not always annotated. One strategy that will probably work is the following: 1. Use FETCH to create a GenBank dataset containing all the genomic and cDNA sequences you want to work with. You might call it X.gen. 2. Subdivide X.gen dataset into two files, cDNA.gen and genomic.gen. (Most of this can be automated using the XYLEM tools.) 3. Extract mRNAs from genomic.gen using the feature key 'mRNA'. Extract mRNAs from cDNA.gen using the feature key 'source' (which will just retrieve the whole thing.) Ideally, 'mRNA' should work for both, but many cDNA entries do not have an mRNA feature key. 4. Check the annotation for all entries to make sure you got what you wanted. 5. Combine the two files into one. =============================================================================== Brian Fristensky | Department of Plant Science | Life doesn't imitate art, University of Manitoba | it imitates bad television. Winnipeg, MB R3T 2N2 CANADA | frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Woody Allen, HUSBANDS AND WIVES FAX: 204-261-5732 | =============================================================================== From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!rutgers!utcsri!yonge.cs.toronto.edu!neuron.ai.toronto.edu!ai.toronto.edu!steeg Newsgroups: bionet.software,bionet.molbio.proteins,bionet.molec-model From: steeg@cs.toronto.edu ("Evan W. Steeg") Subject: Re: Pictures/coordinates for states in protein folding Message-ID: <95Jan5.175343edt.850@neuron.ai.toronto.edu> Originator: root@yonge.cs.toronto.edu Nntp-Posting-Host: yonge.cs.toronto.edu Organization: CS Lab, University of Toronto References: <95Jan4.201837edt.280@neuron.ai.toronto.edu> Distribution: bionet Date: 5 Jan 95 22:54:35 GMT Lines: 53 Xref: biosci bionet.software:10554 bionet.molbio.proteins:3376 bionet.molec-model:222 If I may just follow up on my own posting of yesterday: In article <95Jan4.201837edt.280@neuron.ai.toronto.edu>, Evan W. Steeg wrote: > A friend of mine would like some pictures of a protein in several >different states of folding/unfolding. She'd really prefer Cytochrome C, >but other proteins would suffice. Otherwise, her needs are very >flexible: > > -- Intermediate states may be observed (NMR, etc.) or modelled (according > to some accepted classical/qm simulation model). > > -- Pictures may be space-filling, or ribbon diagrams, or etc. > > -- Pictures in any unix-friendly format (gif, tiff, ppm, etc.) > > In addition to or in lieu of graphics, perhaps there is a database >of partially-folded structures somewhere, akin to the brookhaven pdb >of folded structure coordinate files? I'm curious about this myself. > > Last but not least, can anyone recommend offhand a particularly good >paper on some theoretical or empirical aspects of folding that features >a sequence of pictures as described above (especially of Cyt C!) ? > 1. Lest there be any confusion... what I meant when I referred to various states of folding/unfolding was *well-characterized intermediates in the folding pathway*, and not "unfolded" or "random" configurations. Obviously, it makes no sense to have a database of "unfolded" protein coordinates. 2. I'm making this request for a friend who wants to do a research/reading project for a chemistry course. I talked her into being interested in the protein folding problem (oops) and she is already thinking of how she might give her presentation if she does follow through on this nontrivial topic. It would be nice if she could put up a couple of slides graphically illustrating the ("real" or hypothesized) folding of a particular protein. 3. It occurs to me that, besides my friend's immediate needs, it may be of interest to others (myself included) if there exists any database of either graphics (e.g., a WWW site) or databases of proposed or discovered intermediate structures. Thanks again for your attention. -- Evan Evan W. Steeg (416) 978-5182 steeg@ai.toronto.edu Dept of Computer Science steeg@t13.lanl.gov University of Toronto, Toronto, Canada M5S 1A4 FAX: (416) 978-1455 From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.molbio.rapd,bionet.molbio.yeast,bionet.mycology,bionet.n2-fixation,bionet.neuroscience,bionet.photosynthesis,bionet.plants,bionet.population-bio,bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.users.addresses,bionet.virology,bionet.women-in-bio,bionet.xtallography,biz.americast,biz.books.technical,biz.comp.hardware Path: biosci!bloom-beacon.mit.edu!gatech!newsfeed.pitt.edu!uunet!xnet!quake.xnet.com!research From: crta@xnet.com (Norman Fraley) Subject: New Research & Testing Association Formed Message-ID: Sender: news@amiserv.chi.il.us Nntp-Posting-Host: research.crta.org Organization: Contract Research & Testing Association X-Newsreader: News Xpress Version 1.0 Beta #2 Date: Thu, 5 Jan 1995 20:53:53 GMT Lines: 66 Xref: biosci bionet.molbio.methds-reagnts:22623 bionet.molbio.proteins:3374 bionet.molbio.rapd:925 bionet.molbio.yeast:2110 bionet.mycology:1351 bionet.neuroscience:5641 bionet.photosynthesis:527 bionet.plants:4862 bionet.population-bio:1001 bionet.software:10553 bionet.software.acedb:518 bionet.software.gcg:897 bionet.users.addresses:2135 bionet.virology:1302 bionet.women-in-bio:1694 bionet.xtallography:1410 biz.americast:1037 biz.books.technical:741 biz.comp.hardware:7143 As the primary resource of research information, the Internet was the primary choice for making all concerned individuals aware of the formation of the Contract Research & Testing Association. CRTA is an International Association designed to serve the needs of contract research, product and process development organizations and consultants throughout the world. Contract research organizations have specific public, governmental, and industry perception and promotion needs which are not addressed by existing scientific industry associations. CRTA operates as a non-profit, tax-exempt, corporation eligible for scientific research and public awareness charitable organization contributions as provided for in the IRC 501(c)(3) provisions. Being a scientific research and public awareness related organization, CRTA exists to benefit its members by providing: 1) An organization devoted to the promotion of Contract Research. 2) A unified voice on matters of common interest or concern. 3) Point of contact for media relations relative to contract research. 4) Business opportunity referrals as a research clearinghouse. 5) Professional networking opportunities for its members. 6) Periodic publishing of information beneficial to the membership. 7) Periodic dissemination of applicable research results to the public. 8) Governmental representation on issues affecting CRO's. 9) Public promotion of the strengths of its membership. 10) A directory of Contract Research Organizations and Consultants. CRTA will provide: 1) A forum for the exchange of information. 2) Formal recognition to the CRO's role in business. 3) Standards for the professionals so engaged. 4) Representation the profession in matters of common interest. 5) The development of techniques and methods to improve the practice and management of CROs. CRTA will also offer: 1) A monthly news publication. 2) Annual meetings 3) Active promotional media publicity programs. 4) A professional placement service 5) A Contract Research Service Directory. 6) Media topics and contacts directory If you have an interest in joining the Contract Research & Testing Association, please E-mail your reply to crta@xnet.com. Please include: 1) The word "membership" in your RE: or header information, 2) Your interest in the association / your area of work, 3) Your dues payment preference (check, money order, credit card, company check, wire xfer, etc.) DO NOT INCLUDE ANY CREDIT CARD INFORMATION! Only your preference for the manner of payment. 4) Most importantly, your email address, and additional contact information if you desire. We will then e-mail membership information and ALL FURTHER INFORMATION directly to you at your email location. Thank you for taking the time to read this announcement. If membership in this program this does not appeal to you, thank you for your patience and understanding. Sincerely, Membership Department Contract Research & Testing Association Best Regards, Norman Fraley CRTA@xnet.com Executive Director BBS:708-515-0494 Contract Research & Testing Association From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!evolution.genetics.washington.edu!joe From: joe@evolution.genetics.washington.edu (Joe Felsenstein) Newsgroups: bionet.software Subject: Re: [Q] Is there a mailing list for phylip Date: 5 Jan 1995 20:50:19 GMT Organization: University of Washington, Seattle Lines: 21 Message-ID: <3ehm2b$t7j@news.u.washington.edu> References: <3egl4r$mta@mira.sara.nl> NNTP-Posting-Host: evolution.genetics.washington.edu Summary: Use newsgroups Keywords: PHYLIP mailing list In article <3egl4r$mta@mira.sara.nl> a337hoff@horus.sara.nl (Maurice van den Hoff) writes: >I am a user of the phylip program. I am looking for a mailinglist >of users of this program, who want to share the encountered problems >and how you and we should solve them. The primary method is to e-mail me and I try to help you with the problem. I do quite a lot of that and it is helpful to me to hear what problems people have with the programs. For discussion with a wider audience I would suggest either this newsgroup (bionet.software) or the molecular-evolution group bionet.molbio.evolution. In the long run there will probably be a newsgroup for each major package and in the medium run probably one called something like bionet.software.phylogeny, but the level of traffic is not high enough yet. ----- Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195 Internet: joe@genetics.washington.edu (IP No. 128.95.12.41) From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Newsgroups: bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!rutgers!news.cs.indiana.edu!iedsp@ctf1-5.agt.gmeds.com From: iedsp@ctf1-5.agt.gmeds.com (David S. Pesetsky 230-6088 AGT) Subject: Looking for software... Message-ID: <9501052044.AA26883@ctf1-5.agt.gmeds.com> Sender: root@news.cs.indiana.edu (Operator) Organization: Computer Science, Indiana University Date: Thu, 5 Jan 1995 15:44:37 -0500 Lines: 15 I'm looking for some freeware or shareware to help with cartoons. I'd like to be able to create a cartoon character and quickly show it in different positions, i.e. running, crouching over, from the back, etc... Annimation is not needed. I also am looking for some morphing software. Note: I'm on an IBM RISC6000 running AIX Please respond via e-mail since I don't subscribe to USENET :( iedsp@agt.gmeds.com Thanks! Dave From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.sprintlink.net!EU.net!sun4nl!news.nic.surfnet.nl!news.sara.nl!horus.sara.nl!a337hoff From: a337hoff@horus.sara.nl () Newsgroups: bionet.software Subject: [Q] Is there a mailing list for phylip Date: 5 Jan 1995 11:28:27 GMT Organization: University of Amsterdam Lines: 8 Sender: a337hoff@horus.sara.nl Message-ID: <3egl4r$mta@mira.sara.nl> NNTP-Posting-Host: horus-f.sara.nl Keywords: phylip mailinglist I am a user of the phylip program. I am looking for a mailinglist of users of this program, who want to share the encountered problems and how you and we should solve them. Dr Maurice van den Hoff University of Amsterdam Department of Anatomy and Embryology a337hoff@horus.sara.nl From owner-software@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!library.ucla.edu!agate!overload.lbl.gov!ames!elroy.jpl.nasa.gov!netline-fddi.jpl.nasa.gov!nntp-server.caltech.edu!seqvax.caltech.edu!mathog From: mathog@seqvax.caltech.edu (David Mathog) Newsgroups: bionet.software Subject: Updating databases Date: 5 Jan 1995 12:10 PST Organization: Division of Biolgy, CALTECH Lines: 91 Distribution: world Message-ID: <5JAN199512105050@seqvax.caltech.edu> NNTP-Posting-Host: seqvax.bio.caltech.edu News-Software: VAX/VMS VNEWS 1.41 It would be *really* nice if the folks who maintain and distribute databases would make it a bit easier to automate updates. It isn't all that hard now, but it seems that every time I go to do a set of updates some file has been moved, or changed names, or is .txt.Z when it was just txt the previous time, or in one way or another mutated so as to break my retrieval software. This goal could be accomplished by doing something like the following: 1. At the final FTP/e-mail distribution sites for a particular database place a file that is always called "stub.txt" that contains a retrieval description of that database - all databases to be described in the same format. 2. At several well known sites provide a file "dbs.txt" that contains pointers to the major distribution sites for each database. Example of a stub.txt file: DATABASE:databasename (genbank/pir/swissprot etc.) VERSION:40 (text string) RELEASE_DAY:5 (numeric, day of month) RELEASE_MONTH:12 (numeric, month of year) RELEASE_YEAR:1994 (numeric, full year) NUMBER_OF_FILES:10 (Number of files in full distribution) 1:RETRIEVAL_NAME:example.dat.Z (Valid name on server of first file) 1:RETRIEVAL_METHOD:ftp (ftp or mail) (for FTP) 1:RETRIEVAL_SITE:ftp.somewhere.edu (if blank, same as for stub.txt) 1:RETRIEVAL_PATH: (Relative to stub file, for FTP, here blank) 1:RETRIEVAL_TYPE:binary (text,binary) 1:RETRIEVAL_SIZE: (bytes) (for mail) 1:RETRIEVAL_PIECES:15 (Number of pieces that will come back) 1:RETRIEVAL_TEMPLATE:Example.dat part ## of 15 (What the messages will say) 1:RETRIEVAL_ADDRESS:listserv@somewhere (mail address) 1:RETRIEVAL_SUBJECT:Send example.dat (mail subject line) 1:RETRIEVAL_BODY: (Here, a single blank line) (for either) 1:PROCESS:LZ decompress (UUD, unzip, debinhex, untar, etc.) (Optional: multiple process steps) 1:FINAL_NAME:example.dat (Suggested standard name when installed) 1:FINAL_TYPE:text (text,binary) 1:FINAL_ORGANIZATION:genbank (genbank or embl flatfile, ASN.1,MSWord...) 2:RETRIEVAL_NAME:another.hqx (Valid name on server of second file) etc. Example of a dbs.txt file: DAY:5 (as above - date of this dbs.txt file) MONTH:12 YEAR:1994 DATABASE:databasename (genbank/pir/swissprot etc.) VERSION:40 (text string) DISTRIBUTION_SITES:5 (number of "official" distribution sites) 1:RETRIEVAL_METHOD:ftp (ftp or mail) (etc. Same syntax as for stub.txt, above) 2:RETRIEVAL_METHOD:mail (ftp or mail) etc. DATABASE:nextdatabasename etc. The exact syntax doesn't matter, just keep it simple so that it's trivial to parse using DCL/shell scripts/basic/whatever. Agree on cases so that differences can be used and not trigger on "MONTH" vs. "month" (not a change), but do trigger on "/pub/VMS" vs. "/pub/vms" (is a change). Sites such as ours would use this information to: 1. Periodically check the status of the databases that we maintain by grabbing the latest dbs.txt. Difference it with the last one, if no changes, then quit. If changes are found, then check the version numbers of the databases that we maintain. 2. Retrieve the stub.txt file for each updated database from one of the official distribution sites. Use the information in it to retrieve the database. With this system, database distributors could rearrange their sites, and to some extent, change the names of the files, without breaking everybody's retrieval software, so long as this retrieval software made use of these two types of files. Hmm, with a little care in the syntax this could also be used to handle software distribution, although in that case I'd guess that most of us would want to test the software before having it install automatically over the previous, working copy! Comments? David Mathog mathog@seqvax.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!hookup!uwm.edu!psuvax1!news.pop.psu.edu!hudson.lm.com!netline-fddi.jpl.nasa.gov!nntp-server.caltech.edu!ingber From: ingber@alumni.caltech.edu (Lester Ingber) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.molbio.rapd,bionet.molbio.yeast,bionet.mycology,bionet.n2-fixation,bionet.neuroscience,bionet.photosynthesis,bionet.plants,bionet.population-bio,bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.users.addresses,bionet.virology,bionet.women-in-bio,bionet.xtallography,biz.americast,biz.books.technical,biz.comp.hardware Subject: Re: New Research & Testing Association Formed Date: 6 Jan 1995 14:04:51 GMT Organization: California Institute of Technology, Alumni Association Lines: 165 Message-ID: <3ejim3$eiq@gap.cco.caltech.edu> References: Reply-To: ingber@alumni.caltech.edu NNTP-Posting-Host: alumni.caltech.edu Xref: biosci bionet.molbio.methds-reagnts:22646 bionet.molbio.proteins:3383 bionet.molbio.rapd:927 bionet.molbio.yeast:2117 bionet.mycology:1356 bionet.neuroscience:5655 bionet.photosynthesis:528 bionet.plants:4871 bionet.population-bio:1002 bionet.software:10566 bionet.software.acedb:519 bionet.software.gcg:898 bionet.users.addresses:2136 bionet.virology:1305 bionet.women-in-bio:1699 bionet.xtallography:1412 biz.americast:1044 biz.books.technical:744 biz.comp.hardware:7159 Norman: I like the concept of what you are trying to form, and so I would like to explain why I will not join now, but might be interested at some future time. My criticism is meant to be constructive, and I hope it will be accepted in this context. Since I think your organization is a great idea, I'm making my response public so that other researchers who might be turned off by some of these problems in your presentation also will keep an open mind to joining your organization in the future. (You really did span quite few bulletin boards!) : From crta@xnet.com Thu Jan 5 21:47:00 1995 : Return-Path: : Date: Thu, 5 Jan 1995 23:46:55 -0600 : From: Norman Fraley : To: ingber@alumni.caltech.edu : Subject: Membership information for CRTA : : Dear Mr. Ingber : : WHAT IS CRTA? : : CRTA, formally known as the Contract Research and Testing Association, is : an : international scientific organization whose primary objective is to build : awareness of the role of contract research in industry and in society, : represent the industry in matters of common interest and to provide a forum : for the exchange of ideas and techniques in the fields of Testing and : Applied : Research. If you are appealing to a large audience over the InterNet, you should follow some commonly accepted guidelines, e.g., delivering text in a most readable format, e.g., limiting lines to 79 characters, so that lines do not spill over on most 80-character screens. This is the most vital context of my critique, that you will not come across as a knowledgeable and professional organization unless you present yourself as such. For example, I put your 424-line e-mail reply to my follow-up to this posting through ispell, and here is a partial list which also does not register in `webster`: copywrite lnternational nonanalytical nonmicrobiology proovided spectroscopists toxicologists : CRTA is known for the efforts it has made in helping to promote the new and : rapidly growing industry of contract research. This is accomplished by a : network of nearly 700 commercial, industry, government, and academic : laboratories and individual product and process development consultants. : These promotional activities and other CRTA programs offer you, the : technical : professional, avenues for professional growth and recognition that only an : organization of CRTA's caliber can provide ... plus access to a wellspring : of : analytical, research and technical information. I question whether you already have such a membership, or this is what you aspire to? This is a reasonable question. Many people, like myself, are more sympathetic to an honest statement from a new operation, than to misleading advertisements. I note a number of journals and publications you (intend to?) make available, and I expect they have a price. Your fees for members of $125/yr is fair, if all these services are available now. All this is fine, but those prices should be stated up front. : Email: crta@xnet.com : WWW: www.xnet.com/~crta I tried this site, http://www.xnet.com/~crta, and found a short notice that it is under construction. I think it better to first do your homework, before advertising such a site, especially since you really are charging commercial rates for a commercial venture, your non-profit status notwithstanding. : copywrite 1994 Contract Research & Testing Association. This one is a real killer, demonstrating that you are not sensitive to one of the main concerns of contract research, the copyright (not the "copywrite"). Lester In article , Norman Fraley wrote: :As the primary resource of research information, the Internet was the :primary choice for making all concerned individuals aware of the formation :of the Contract Research & Testing Association. : :CRTA is an International Association designed to serve the needs of contract :research, product and process development organizations and consultants :throughout the world. Contract research organizations have specific public, :governmental, and industry perception and promotion needs which are not addressed :by existing scientific industry associations. CRTA operates as a non-profit, :tax-exempt, corporation eligible for scientific research and public awareness :charitable organization contributions as provided for in the IRC 501(c)(3) provisions. : :Being a scientific research and public awareness related organization, CRTA :exists to benefit its members by providing: : : 1) An organization devoted to the promotion of Contract Research. : 2) A unified voice on matters of common interest or concern. : 3) Point of contact for media relations relative to contract research. : 4) Business opportunity referrals as a research clearinghouse. : 5) Professional networking opportunities for its members. : 6) Periodic publishing of information beneficial to the membership. : 7) Periodic dissemination of applicable research results to the public. : 8) Governmental representation on issues affecting CRO's. : 9) Public promotion of the strengths of its membership. : 10) A directory of Contract Research Organizations and Consultants. : :CRTA will provide: : 1) A forum for the exchange of information. : 2) Formal recognition to the CRO's role in business. : 3) Standards for the professionals so engaged. : 4) Representation the profession in matters of common interest. : 5) The development of techniques and methods to improve the practice and : management of CROs. : :CRTA will also offer: : 1) A monthly news publication. : 2) Annual meetings : 3) Active promotional media publicity programs. : 4) A professional placement service : 5) A Contract Research Service Directory. : 6) Media topics and contacts directory : :If you have an interest in joining the Contract Research & Testing Association, :please E-mail your reply to crta@xnet.com. Please include: : :1) The word "membership" in your RE: or header information, :2) Your interest in the association / your area of work, :3) Your dues payment preference (check, money order, credit card, company check, wire xfer, etc.) : DO NOT INCLUDE ANY CREDIT CARD INFORMATION! Only your preference for the manner of payment. :4) Most importantly, your email address, and additional contact information if you desire. : :We will then e-mail membership information and ALL FURTHER INFORMATION :directly to you at your email location. Thank you for taking the time :to read this announcement. If membership in this program this does not :appeal to you, thank you for your patience and understanding. : :Sincerely, :Membership Department :Contract Research & Testing Association : : :Best Regards, : :Norman Fraley CRTA@xnet.com :Executive Director BBS:708-515-0494 :Contract Research & Testing Association -- /* Prof. Lester Ingber * * Lester Ingber Research E-Mail: ingber@alumni.caltech.edu * * P.O. Box 857 WWW: http://alumni.caltech.edu/~ingber/ * * McLean, VA 22101 Archive: ftp.alumni.caltech.edu:/pub/ingber/ */ From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Newsgroups: bionet.software Path: biosci!CS.Arizona.EDU!uunet!spool.mu.edu!torn!nott!cunews!freenet.carleton.ca!FreeNet.Carleton.CA!aj519 From: aj519@FreeNet.Carleton.CA (Robert W Beggs) Subject: Problem with NCBI Gene Server???? Message-ID: Sender: aj519@freenet.carleton.ca (Robert W Beggs) Reply-To: aj519@FreeNet.Carleton.CA (Robert W Beggs) Organization: The National Capital FreeNet Date: Fri, 6 Jan 1995 02:41:56 GMT Lines: 24 Netters - Ive been trying to log onto the NCBI gene server (retrieve@ncbi.nlm.nih.gov) to download some gene sequences> The body of the message I've used has been: DATALIB gb MAXDOCS 999 MAXLINES 9999 TITLES BEGIN bacillus The server has refused to accept these arguments, and keeps sending me error messages, or copies of the RETRIEVE help document...does anyone know what I'm doing wrong? Robb Beggs -- "...For my purpose holds | Robert W. Beggs To sail beyond the sunset, and the baths | aj519@freenet.carleton.ca Of all the western stars, until I die." | (613) 724-1169 (Home) - Alfred Lord Tennyson | From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!cs.utexas.edu!howland.reston.ans.net!news.starnet.net!wupost!kuhub.cc.ukans.edu!kuhub.cc.ukans.edu!nntp Newsgroups: bionet.software Subject: Re: Scatchard Analysis Software Message-ID: <1995Jan5.181844.81924@kuhub.cc.ukans.edu> From: peterg@rnaworld.bio.ukans.edu (Peter Gegenheimer) Date: 5 Jan 95 18:18:43 CST Reply-To: pgegen@kuhub.cc.ukans.edu (Peter Gegenheimer) References: <3ehenh$fbr@lastactionhero.rs.itd.umich.edu> Distribution: world Organization: Dept. Biochemistry, Univ. Kansas-Lawrence KS Nntp-Posting-Host: rnaworld.bio.ukans.edu X-Newsreader: IBM NewsReader/2 v1.02 Lines: 54 In <3ehenh$fbr@lastactionhero.rs.itd.umich.edu>, Chris Beecher writes: >I am looking for PC or Mac software that can do a Scatchard analysis for >at least one-site ligand binding experiments. > > >I am already familair with Ligand and it barely gets by, can anyone >recommend something better without spending an arm and a leg? > >chris beecher >Univ of Mich Ligand binding is not determined from a Scatchard plot but from least-squares non-linear regression fitting of the hyperbolic binding curve to the raw data (bound ligand vs total ligand). For a simple example, see Chen et al, FEBS Lett. 298, 69-73 (1992). Any sort of linear transformation of the data introduces statistical errors which make the results less reliable than direct curvefitting to the unmanipulated data. This is especially true for a Scatchard plot, in which calculation of [free ligand] is often unreliable at very low [total ligand]. The *easiest* program for non-linear curvefitting is the old PC program Enzfitter (BioSoft; avail from Sigma and other scientific software distributors). Enzfitter is expensive ($250-350) but lets you enter your own equations; it uses linear transforms, if possible, to obtain initial estimates for the non-linear curvefitting. It also lets you adjust the type of robust weighting. It has excellent graphing capabilities; they require work and are not publication-quality, but you can transfer everything to s simple plotting program for final figures if necessary. A slick (and $$) versions of this program are Graft-It for Windows, and Ultra-Fit for the Mac. Probably mush easier to use, but I haven't tried them. The *cheapest* way is to use the freeware program Hyper (for Windows). It's available from ftp sites; I don't remember which one (maybe IUBio?) Hyper will fit to the Michaelis-Menten equation, which is a plot of [bound ligand] vs [total ligand] for any ligand which is not a substrate. Hyper is excellent in that it also plot all the common linear transforms (Lineweaver-Burk; Eadie-Hofstee-Scatchard; Haines-Woolfe) to let you see how their answers differ from the true answer. A compromise is to use any one of the many scientific graphing programs which have built-in non-linear curvefitting capabilities. SigmaPlot is one; PSI Plot (only $50 academic) is my favorite. These curvefitters require a little work to set up the equations, especially if you want to use robust weighting. If you can get the $, get Enzfitter or a similar program. You'll use it constantly. o------------------------------------------------------------------------o | Peter Gegenheimer | pgegen@kuhub.cc.ukans.edu | | Departments of Biochemistry | voice: 913-864-3939 | | and of Botany | | | University of Kansas | FAX : 913-864-5321 | | 2045 Haworth Hall | "The sleep of reason produces | | Lawrence KS 66045-2106 | monsters." Goya | o_______________________________|________________________________________o From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!news.sprintlink.net!redstone.interpath.net!mercury.interpath.net!not-for-mail From: morgan@mercury.interpath.net (Morgan Ryan) Newsgroups: bionet.software Subject: pdb->dxf, anything else? Date: 5 Jan 1995 21:02:47 -0500 Organization: Interpath -- Public Access UNIX for North Carolina Lines: 5 Message-ID: <3ei8c7$r6j@mercury.interpath.net> NNTP-Posting-Host: mercury.interpath.net I'm trying to find a utility that will convert pdb files into dxf 3d files. Conversion to _any_ 3d format would be OK, since there are a zillion anyhing->anything converters out there. I just can't find one that gets me off first base--the pdb file. Thanks, Morgan Ryan From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!biosci!not-for-mail From: ayoung@vax.oxford.ac.uk (Geordie +1865 740 011) Newsgroups: bionet.software,bionet.announce Subject: version 1.2 of GAS now available Date: 5 Jan 1995 16:49:30 -0800 Organization: Oxford University VAX 6620 Lines: 33 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: <1995Jan5.135549.28277@oxvaxd> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:10555 bionet.announce:1663 The GAS program has now been updated to Version 1.2, which is available via anonymous ftp from well.ox.ac.uk in directory pub/genetics/gas. For users new to this package, it provides facilities for reading, writing, sectioning and performing statistical analyses on phenotypic and genotypic data. It has been developed within the department of medicine at Oxford University and is available via ftp as freeware. The main additions to the previous version include: * full use of extended memory on IBM 486/Pentium PCs * association tests for marker/candidate alleles and diseases * extended categories of select(), including marker alleles * maximum-likelihood estimates for sib-pair IBD In response to requests the section of the manual devoted to the select() command has been enlarged with further examples. A minor bug gas been corrected in 1.1 sibstate(). This was giving too low p-values and has been corrected in version 1.2. No other bugs were reported. Directions for unpacking the program and documentation are in the file `README' available via anonymous ftp from directory pub/genetics/gas at well.ox.ac.uk -- ------------------------------------------------------------------------------- ___ / \ / | / Alan Young @ uk.ac.ox.vax /____/ / ___ __ |___/ / / / / | / | / "The bigger they are, / \_/\__\__/|_/ /_________/ the harder they fall on you." From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!warwick!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.software Subject: GCG/SRS Date: 6 Jan 1995 13:44:31 -0000 Lines: 40 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3ejhfv$pgr@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk Hello netters, First of all, happy new year to all of you. Second: I have a problem with SRS. I sent mails to T. Etzold and P. Rice but in the absence of answers (so far) I'm trying to get help from the gurus on the net. Here it is: In a recent weekly update of the EBI databank appeared the sequences of yeast chromosome II and a long E. coli contig, both of them having more than 350,000 bp. As you know, GCG will split them into 2 parts. Now, the second part of the GCG formatted files contains NO accession number. When SRS builds its indices from the GCG files, it is confused by the absence of AC (at least that's what I understand) and it crashes. Very very ennoying... Have you any idea? Can somebody help me? I'm somewhat reluctant to simply remove these sequences from the flat file, which in any case could be only a very temporary fix... Thank you Jean-Loup --------------------------------------------------------------------- Jean-Loup Risler Tel: (33 1) 69 82 31 34 CNRS Fax: (33 1) 69 07 49 73 Centre de Genetique Moleculaire Email: risler@cgmvax.cgm.cnrs-gif.fr 91198 Gif sur Yvette Cedex France --------------------------------------------------------------------- From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!Germany.EU.net!EU.net!uknet!comlab.ox.ac.uk!oxuniv!ayoung From: ayoung@vax.oxford.ac.uk (Geordie +1865 740 011) Newsgroups: bionet.software Subject: version 1.2 of GAS now available Message-ID: <1995Jan6.112204.28289@oxvaxd> Date: 6 Jan 95 11:22:04 GMT Organization: Oxford University VAX 6620 Lines: 35 The GAS program has now been updated to Version 1.2, which is available via anonymous ftp from well.ox.ac.uk in directory pub/genetics/gas. For users new to this package, it provides facilities for reading, writing, sectioning and performing statistical analyses on phenotypic and genotypic data. It has been developed within the department of medicine at Oxford University and is available via ftp as freeware. Implementations of GAS are currently available for: IBM PCs (DOS), DEC Alphas, DEC Ultrix, Sun Solaris, SunOS and Vax VMS systems. The main additions to the previous version include: * full use of extended memory on IBM 486/Pentium PCs * association tests for marker/candidate alleles and diseases * extended categories of select(), including marker alleles * maximum-likelihood estimates for sib-pair IBD In response to requests the section of the manual devoted to the select() command has been enlarged with further examples. A minor bug gas been corrected in 1.1 sibstate(). This was giving too low p-values and has been corrected in version 1.2. No other bugs were reported. Directions for unpacking the program and documentation are in the file `README' available via anonymous ftp from directory pub/genetics/gas at well.ox.ac.uk -- ------------------------------------------------------------------------------- ___ / \ / | / Alan Young @ uk.ac.ox.vax /____/ / ___ __ |___/ / / / / | / | / "The bigger they are, / \_/\__\__/|_/ /_________/ the harder they fall on you." From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!news.uni-c.dk!codon!gorm From: gorm@codon (Anders Gorm Pedersen) Newsgroups: bionet.software Subject: Re: cDNA extracton from feature tables Date: 6 Jan 1995 12:04:20 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 65 Distribution: world Message-ID: <3ejbk4$pbi@news.uni-c.dk> References: <3egflf$356@mserv1.dl.ac.uk> <3ehji3$kat@canopus.cc.umanitoba.ca> NNTP-Posting-Host: codon.cbs.fki.dth.dk X-Newsreader: TIN [version 1.2 PL1] Brian Fristensky (frist@cc.umanitoba.ca) wrote: : In article 356@mserv1.dl.ac.uk, "Taylor Mr S" () writes: : > I seem to remember some time ago I saw some freeware which allowed you : > to extract relevant information from EMBL or Genbank database entry : > feature tables. : > : See the XYLEM package which is available by anonymous FTP to directory 'psgendb' : at ftp.cc.umanitoba.ca. The FEATURES program can extract any feature annotated : in a GenBank entry, and even extract unannotated regions given user-supplied : Feature expressions. A complete description of this process can be found in : Fristensky, B. (1993) Feature expressions: creating and manipulating : sequence datasets. Nucl. Acids Res. 21:5997-6003. : > I would like to be able to pull out full length cDNAs from a collection of : > database entries and don't want to have to examine every feature table : > by hand to find where the exons are ! Anything that does : > this sort of operation would be useful. : > Steve Taylor, : > Glaxo R & D, : > England : > : It's not entirely clear what you mean here. cDNAs per se do not have introns : to remove. Do you mean to say that you wish to extract a set of mRNAs from : entries containing either cDNAs or genomic sequences? : There is no feature key for cDNAs as such, but : extracting using the 'mRNA' feature key will work where mRNA has been annoted : in the GenBank entry. Unfortunately, it is not always annotated. : One strategy that will probably work is the following: : 1. Use FETCH to create a GenBank dataset containing all the genomic and cDNA : sequences you want to work with. You might call it X.gen. : 2. Subdivide X.gen dataset into two files, cDNA.gen and genomic.gen. (Most of : this can be automated using the XYLEM tools.) : 3. Extract mRNAs from genomic.gen using the feature key 'mRNA'. Extract : mRNAs from cDNA.gen using the feature key 'source' (which will just : retrieve the whole thing.) Ideally, 'mRNA' should work for both, but : many cDNA entries do not have an mRNA feature key. : 4. Check the annotation for all entries to make sure you got what you wanted. : 5. Combine the two files into one. : =============================================================================== : Brian Fristensky | : Department of Plant Science | Life doesn't imitate art, : University of Manitoba | it imitates bad television. : Winnipeg, MB R3T 2N2 CANADA | : frist@cc.umanitoba.ca | : Office phone: 204-474-6085 | Woody Allen, HUSBANDS AND WIVES : FAX: 204-261-5732 | : =============================================================================== -- Anders Gorm Pedersen Center for Biological Sequence Analysis, Technical University of Denmark Phone: (+45) 45 93 12 22 ext. 2471 (tone). Fax: (+45) 45 93 48 08 e-mail: gorm@cbs.dth.dk From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!uunet!spool.mu.edu!howland.reston.ans.net!news.sprintlink.net!news.world.net!serval.net.wsu.edu!netnews.nwnet.net!news.u.washington.edu!root From: Bassuk@U.Washington.Edu (Jim Bassuk) Newsgroups: bionet.software Subject: Digital chromatograms: Parts list? Date: 6 Jan 1995 08:02:56 GMT Organization: University of Washington Lines: 39 Message-ID: <3eitfg$o29@nntp1.u.washington.edu> NNTP-Posting-Host: stein2.u.washington.edu X-Newsreader: WinVN 0.92.5 Path: news.u.washington.edu!root From: Bassuk@U.Washington.Edu (Jim Bassuk) Newsgroups: bionet.molbio.proteins Subject: Digital chromatograms: parts list? Date: 6 Jan 1995 07:55:26 GMT Organization: University of Washington Lines: 21 Message-ID: <3eit1e$o29@nntp1.u.washington.edu> NNTP-Posting-Host: stein2.u.washington.edu X-Newsreader: WinVN 0.92.5 In standard chromatography of proteins, we monitor the absorbance of the column eluate with a Pharmacia UV-1 flow cell coupled to a chart recorder. This analog signal from the UV-1 is 10 mV. To design a system to convert the signal to a digital format, I'll need a A/D converter, some sort of board for a yet-to-be purchased 486 PC, and some sort of software to acquire, process, and store the data. We'll likely couple two UV-1 units in tandem (214 and 280 nm).....this is 2 channels.....and then a simple closure switch to indicate the advancement of the fraction collector....this is another channel... a total of 3 channels..... No need to buy a big, expensive HPLC software program, because I won't be controlling any pumps, etc... Comments on boards, A/D units, and software sources and experiences are respectfully requested. Thanks in advance, Jim Bassuk BioStructure Univ Washington Go Bears! From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!CS.Arizona.EDU!uunet!fdn.fr!jussieu.fr!univ-lyon1.fr!grenet.fr!usenet From: hewat@ill.fr (Alan Hewat) Newsgroups: bionet.software Subject: Re: pdb->dxf, anything else? Date: 6 Jan 1995 07:55:07 GMT Organization: ILL Grenoble France (High Flux European Research Reactor) Lines: 19 Sender: hewat@onyx.ill.fr Message-ID: <3eit0r$pp7@cicg-communication.grenet.fr> References: <3ei8c7$r6j@mercury.interpath.net> NNTP-Posting-Host: machew.ill.fr X-Posted-From: InterNews 1.0.4@machew.ill.fr X-Authenticated: hewat on POP host onyx.ill.fr morgan@mercury.interpath.net (Morgan Ryan) writes: > I'm trying to find a utility that will convert pdb files into dxf 3d > files. Conversion to _any_ 3d format would be OK, since there are a > zillion anyhing->anything converters out there. I just can't find one > that gets me off first base--the pdb file. Thanks, Morgan Ryan I have almost finished an application (xtal-3d) that reads a number of crystallographic formats including pdb and produces 3D Inventor files. There is a free dxf to Inventor file transformer (dxf2iv) available from sgi.com, but not iv2dxf so far as I know. xtal-3d will display the Inventor files as 3D objects that can be rotated and zoomed in real time on any system that has an Inventor viewer (at present only Silicon Graphics, but soon Windows-NT and other systems). If you are interested in knowing more about xtal-3d, send me an email. Alan Hewat, ILL Grenoble, FRANCE (hewat@ill.fr) Fax (33) 76.48.39.06 From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Newsgroups: bionet.software Path: biosci!CS.Arizona.EDU!uunet!bloom-beacon.mit.edu!usc!howland.reston.ans.net!agate!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: cDNA extracton from feature tables Message-ID: <1995Jan6.074008.13913@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <3egflf$356@mserv1.dl.ac.uk> Distribution: bionet Date: Fri, 6 Jan 1995 07:40:08 GMT Lines: 28 Taylor Mr S (st23646@ggr.co.uk) wrote: [...] : I would like to be able to pull out full length cDNAs from a collection of : database entries and don't want to have to examine every feature table : by hand to find where the exons are ! Anything that does : this sort of operation would be useful. The SRS database browser is available as software for local installation or can be accessed via the world-wide web at 9 nodes worldwide. SRS mother page is on http://www.embl-heidelberg.de/srs/srsc and was written by Thure Etzold, EMBL Heidelberg. SRS can extract CDS from entire sequende databases and combine, map, filter with whatever database or database query you want (currently, > 50 databases. Check out http://www.ch.embnet.org/srs/status.html for reference). Regards Reinhard Doelz EMBnet Switzerland -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!MCZ.HARVARD.EDU!dmw From: dmw@MCZ.HARVARD.EDU (Daniel Weinreich) Newsgroups: bionet.software Subject: Re: Problem with NCBI Gene Server???? Date: 6 Jan 1995 10:55:31 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3ek043$e3k@decaxp.harvard.edu> NNTP-Posting-Host: net.bio.net On 6 Jan 1995, Keith Robison wrote: > Robert W Beggs (aj519@FreeNet.Carleton.CA) wrote: > : Netters - > > : Ive been trying to log onto the NCBI gene server > &&&&&&&&& > please say E-mail, at first I thought you really tried to log on > > : (retrieve@ncbi.nlm.nih.gov) to download some gene sequences> The body of > : the message I've used has been: > > : DATALIB gb > : MAXDOCS 999 > : MAXLINES 9999 > : TITLES > : BEGIN > : bacillus > > Try DATALIB Genbank > ^^^^^^^ gb is fine. > Also, I always say "TITLES yes" -- but this may not be necessary It's not. I missed the original post, and got 48 docs back when I tried your message. Exactly what kind of error did you get? Two further suggestions: get the NCBI help doc by sending message with the single word "help" in the body. And don't be shy about writing the staff directly at retrieve-help@ncbi.nlm.nih.gov; in my experience they're competent and quick to reply. ------------------------------------------------------------------- Daniel M. Weinreich email: dmw@mcz.harvard.edu Harvard University usmail: 26 Oxford Street Museum of Comparative Zoology Cambridge, MA 02138 voice: (617) 495-1954 fax: (617) 495-5667 ------------------------------------------------------------------- From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!news2.near.net!das-news2.harvard.edu!fas-news.harvard.edu!lipid!robison From: robison@lipid.harvard.edu (Keith Robison) Newsgroups: bionet.software Subject: Re: Problem with NCBI Gene Server???? Date: 6 Jan 1995 17:54:11 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 39 Message-ID: <3ek043$e3k@decaxp.harvard.edu> References: NNTP-Posting-Host: lipid.harvard.edu X-Newsreader: TIN [version 1.2 PL2] Robert W Beggs (aj519@FreeNet.Carleton.CA) wrote: : Netters - : Ive been trying to log onto the NCBI gene server &&&&&&&&& please say E-mail, at first I thought you really tried to log on : (retrieve@ncbi.nlm.nih.gov) to download some gene sequences> The body of : the message I've used has been: : DATALIB gb : MAXDOCS 999 : MAXLINES 9999 : TITLES : BEGIN : bacillus Try DATALIB Genbank ^^^^^^^ Also, I always say "TITLES yes" -- but this may not be necessary For better or worse, the RETRIEVE server doesn't recognize a lot of common abbreviations for databases. Also, you can get all the functionality of RETRIEVE with some added features using the Web interface. See NCBI's server for details: http://www.ncbi.nlm.nih.gov/ Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@mito.harvard.edu From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!newsfeed.pitt.edu!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!inherit.lmb.uni-muenchen.de!user From: steipe@lmb.uni-muenchen.de (Boris Steipe) Newsgroups: bionet.software Subject: Re: Scatchard Analysis Software Followup-To: bionet.software Date: 6 Jan 1995 15:54:06 GMT Organization: Genzentrum, biostructure lab Lines: 14 Distribution: world Message-ID: References: <3ehenh$fbr@lastactionhero.rs.itd.umich.edu> <1995Jan5.181844.81924@kuhub.cc.ukans.edu> NNTP-Posting-Host: 141.84.48.171 In article <1995Jan5.181844.81924@kuhub.cc.ukans.edu>, peterg@rnaworld.bio.ukans.edu (Peter Gegenheimer) wrote: [snip] > software distributors). Enzfitter is expensive ($250-350) but lets you enter > your own equations; it uses linear transforms, if possible, to obtain initial > estimates for the non-linear curvefitting. It also lets you adjust the type > of robust weighting. It has excellent graphing capabilities; they require [snip] ... we use KaleidaGraph on the Mac, you can also enter your own formulas for non-linear least square fit and the plots are of excellent quality. -- Boris From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.sprintlink.net!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!inherit.lmb.uni-muenchen.de!user From: steipe@lmb.uni-muenchen.de (Boris Steipe) Newsgroups: bionet.software Subject: Re: metal-binding sites Followup-To: bionet.software Date: 6 Jan 1995 15:27:12 GMT Organization: Genzentrum, biostructure lab Lines: 37 Distribution: world Message-ID: References: <9501041949.AA28566@silibone.cchem.berkeley.edu> NNTP-Posting-Host: 141.84.48.171 In article <9501041949.AA28566@silibone.cchem.berkeley.edu>, yang@SILIBONE.CCHEM.BERKELEY.EDU wrote: > > We are looking for programs which search backbone structures for metal-binding > sites--specifically, we are interested in "designing" such sites in > non-metallo enzymes in order to improve catalysis. Thanks in advance! You're probably aware of WHATIF by G.Vriend - if not, check Vriend, J.Mol.Graph, 8:52-56, and Proteins Struct.Funct. Genet. 11:52-58. To obtain a licence, contact . This should help with identifying binding sites. The question of how to put ligand binding sites into your protein is a different matter. You need to identify those residues of your target structure, which are closest in 3D structure to the binding site. But you know in advance neither where these residues are going to be, nor even in what order they should be in the target sequence. For example, a three His zinc binding site may be -1-..-2-..-3- in the binding site from the database, while the closest structural correspondence in your target sequence might be -2-..-1-..-3- and with the residues on totally different elements of secondary structure. What this amounts to is a combinatorial search of _all_ possible replacements and then checking which replacement will give the best fit. Then you can find those which are plausibly close to your active site among well fitting candidates. The problem is of course that the number of tests you have to do explodes (it is n!-(n-i)! with n the size of your protein sequence and i the size of your binding site, which for a site of 6 residues tested against a protein of 200 residues is 6*10^13) A while ago I wrote a program to do this kind of test efficiently. Contact me if you need further information. Best wishes -- Boris From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!cs.utexas.edu!uunet!news.unr.edu!ub!acsu.buffalo.edu!burkhart From: burkhart@mfb.buffalo.edu (Brian M Burkhart) Subject: DOCK and related programs Message-ID: Originator: burkhart@galen.hwi.buffalo.edu Sender: nntp@acsu.buffalo.edu Nntp-Posting-Host: galen.hwi.buffalo.edu Organization: Medical Foundation of Buffalo Date: Fri, 6 Jan 1995 14:34:06 GMT Lines: 14 Our group is interested in doing some drug design and docking studies. Could the net please inform me as to possible programs for doing such work. I am aware of the MSI programs and I know of DOCK but I do not know who to contact regarding it. MAny thanks Brian Burkhart -- ----- ----- / / / / / / / / From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!scripps.edu!usenet From: johnson@riscsm.scripps.edu Newsgroups: bionet.software Subject: Re: DOCK and related programs Date: 6 Jan 1995 19:01:56 GMT Organization: The Scripps Research Institute Lines: 27 Message-ID: <3ek434$2lf@riscsm.scripps.edu> References: Reply-To: johnson@riscsm.scripps.edu NNTP-Posting-Host: kestrel_pc.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: IBM NewsReader/2 v1.02 In , burkhart@mfb.buffalo.edu (Brian M Burkhart) writes: > >Our group is interested in doing some drug design and >docking studies. Could the net please inform me as to >possible programs for doing such work. I am aware of the >MSI programs and I know of DOCK but I do not know who to >contact regarding it. > The following is taken from the www site for DOCK. It can be reached through the home page for the Kunz group at: http://www.cmpharm.ucsf.edu/kuntz/kuntz.html The most recent version of DOCK is DOCK3.0 Dock is freely available to academic institutions, but is licensed with a charge to industry. To obtain DOCK please contact Paul McCloskey at (415) 476-9031 or mcclosk@cgl.ucsf.edu Paul McCloskey Box 0446 UCSF--Molecular Design Institute 513 Parnassus, Room U64-B University of California San Francisco, California 94143-0446 From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Newsgroups: bionet.software Path: biosci!CS.Arizona.EDU!uunet!cs.utexas.edu!howland.reston.ans.net!agate!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: Updating databases Message-ID: <1995Jan6.073436.13810@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <5JAN199512105050@seqvax.caltech.edu> Date: Fri, 6 Jan 1995 07:34:36 GMT Lines: 83 David Mathog (mathog@seqvax.caltech.edu) wrote: : It would be *really* nice if the folks who maintain and distribute : databases would make it a bit easier to automate updates. It isn't all : that hard now, but it seems that every time I go to do a set of updates : some file has been moved, or changed names, or is .txt.Z when it was just : txt the previous time, or in one way or another mutated so as to break my : retrieval software. [...] : Comments? Comment 1: The proposed stubs try to compensate the weakness of a transaction based on a poll mechanism without query. Rather than the customer inquires in detailed fashion, the current schema of FTP requires the FTP site to be (1) fixed in file names (btw, what do you do with your software if a new division appears), (2) preprepared for any request, be it day-by-day, week-by-week, or other, and (3) does not at all tackle the question what to do with it. The proposed schema does not mention whether the target is to update (1) formatted (which format? ), (2) unformatted or (3) incremental data. In particular, the latter is most appropriate at wide area networks to save badnwith, and raises management problems at the local site. Comment 2: The proposed schema seems to imply a resource discovery based on static listings. These are notoriously difficult to maintain and do not necessarily offer a quality control issue (see below). Even if this were a possibility, this implied that all sites referencing each other have the same policy of 'free for all' and do honor the same quality standards. Comment 3: The major problem in sequence database updating is that the quality of an update cannot be judged if you download it as file. Neither date nor contents are sufficiently characterized in their format. A synchronisation is required (or at least desirable) which allows to crosscheck the contents of your local, adapted , formatted copy to the originally present data at the provider. Versions and dates are nice but insufficient to characterize a contents in incremental updates. Comment 4: The proposed schema requires a considerable amount of coordination in between providers. The resources for the update buisness are fairly low as you, and many others, are neither prepared nor willing to pay for the service you request. I'm not telling you that all researchers ought to be tapped but as I had to realize recently lots of our customers don't even know where the data come from, and being asked for funding, the granting organizations want to bless just these customers with 'self-sustaining' fees to cover the costs of such a service. In other words, even if the items 1-3 could be ruled out, money is tough. Comment 5: The market is fairly small. In Europe, we have 26 EMBnet nodes mirroring the EMBL database, and presumably about 100 sites who care about updates. The recent referee's comment on a paper we submitted to XXXXX with respect to a new compression system was (quote) "Not many sites update their databases regularly over the Internet". This might be a guess on the low side but you will not be able to count on commercial providers to help you developing such a mechanism easily. Comment 6: We are aware of all these problems. We deal with them on a daily basis as we update all sequence databases available on daily, or weekly schedule. We have developed suitable mechanisms to receive, distribute and redistribute updates. The reason why we didn't make it a 'release' yet is the resource issue - it works for us, and not necessarily requires that we make the methods publically available. I am currently finishing HASSLE with SRS access but afterwards will try to work on the DBTOOLS for release in early summer (sorry it was originally scheduled fall '94 but postponed). This should be symptomatic as it shows that once it works at the local site any effort to make it used on a wider basis in not profitable for the individual site and therefore usually not practiced heavily. Regards Reinhard Doelz EMBnet Switzerland -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!UNIXG.UBC.CA!mleroux From: mleroux@UNIXG.UBC.CA (Mleroux@unixg.ubc.ca) Newsgroups: bionet.software Subject: RE: STRUCTURAL PROTEIN SIMILARITY PROGRAM Date: 6 Jan 1995 15:57:39 -0800 Organization: Bangkok Security Associates Lines: 56 Sender: daemon@net.bio.net Distribution: world Message-ID: <9501070701026002@wov.com> NNTP-Posting-Host: net.bio.net From: mleroux@unixg.ubc.ca (Michel Leroux) Subject: Re: Structural protein similarity program Date: 5 Jan 1995 17:08:39 GMT In article , floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) wrote: > Hi! > > I'm looking for public domain programs for structure-structure alignments and > for the identification of structural similarities in protein folds. The > program should run on either SGI or Dec-Alpha (in the worst case on > MS-DOS PC's). > > Anyone who knows a program to do structure-strucutre alignment? > > Thanx > Hannes Yes, I know of a program which may be just what you're looking for. It's called PHD, and its purpose is to predict the secondary structure of any given protein, and it also takes into account other similar (homologous) protein sequences. The more sequences it can compare to from the protein database, the better the prediction. They give a reference which claims the prediction is about 70% accurate. I have recently used it and found that the predicted GroEL secondary structure is VERY similar to the known secondary structure of this protein. It's available on any platform, and is very easy to use because it's a free e-mail service. All you need to do is send the following e-mail message: ------------------------------------------- To: PredictProtein@embl-heidelberg.de your name your address your e-mail address predict secondary structure # protein_name MAFGIHRTIPECV...(etc., your protein sequence) ------------------------------------------- You receive a confirmation of your request promptly, and then about half an hour later you get the secondary structure prediction. In your case, you'd have to compare the secondary structures manually, but this should serve your needs adequately. Michel Leroux mleroux@unixg.ubc.ca From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!usenet From: billh@lisboa.ks.uiuc.edu (William F. Humphrey) Newsgroups: bionet.software Subject: compiling RasMol 2.5 for HP-UX Date: 6 Jan 1995 20:58:49 GMT Organization: University of Illinois at Urbana Lines: 36 Message-ID: <3ekau9$4gd@vixen.cso.uiuc.edu> NNTP-Posting-Host: napoli.ks.uiuc.edu Hi - Anybody managed to compile RasMol 2.5 for HP-UX 9.05? My rather quick attempt to do this yielded the following problem: prospero:billh [40] % xmkmf mv Makefile Makefile.bak imake -DUseInstalled -I/usr/local/lib/imake prospero:billh [41] % make cc +O2 +Onolimit -Ae -I/usr/include/X11R5 -I/usr/local/include -DSYSV -Dhpux -DRASMOLDIR=\"/usr/lib/X11R5 -L/usr/lib/X11R4/rasmol/\" -DEIGHTBIT -c rasmol.c cc +O2 +Onolimit -Ae -I/usr/include/X11R5 -I/usr/local/include -DSYSV -Dhpux -DRASMOLDIR=\"/usr/lib/X11R5 -L/usr/lib/X11R4/rasmol/\" -DEIGHTBIT -c molecule.c cc +O2 +Onolimit -Ae -I/usr/include/X11R5 -I/usr/local/include -DSYSV -Dhpux -DRASMOLDIR=\"/usr/lib/X11R5 -L/usr/lib/X11R4/rasmol/\" -DEIGHTBIT -c abstree.c cc +O2 +Onolimit -Ae -I/usr/include/X11R5 -I/usr/local/include -DSYSV -Dhpux -DRASMOLDIR=\"/usr/lib/X11R5 -L/usr/lib/X11R4/rasmol/\" -DEIGHTBIT -c command.c cc: "command.c", line 761: error 1004: Unexpected end of line. *** Error code 1 If anyone has successfully done this, I would be very interested in and appreciative for the information on how to finish the compilation. Thanks ... -- /* Bill Humphrey (billh@ks.uiuc.edu) */ /* Theoretical Biophysics | Nothing matters but */ /* Beckman Institute - U. of Illinois | the weekend, from a */ /* 405 North Matthews | Tuesday point of view */ /* Urbana, IL 61801 | */ /* phone: (217) 244-1851 | fax: (217) 244-6078 */ From owner-software@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!agate!ames!elroy.jpl.nasa.gov!netline-fddi.jpl.nasa.gov!nntp-server.caltech.edu!seqvax.caltech.edu!mathog From: mathog@seqvax.caltech.edu (David Mathog) Newsgroups: bionet.software Subject: Re: Updating databases Date: 6 Jan 1995 11:59 PST Organization: Division of Biolgy, CALTECH Lines: 92 Distribution: world Message-ID: <6JAN199511593309@seqvax.caltech.edu> References: <5JAN199512105050@seqvax.caltech.edu> <1995Jan6.073436.13810@comp.bioz.unibas.ch> NNTP-Posting-Host: seqvax.bio.caltech.edu News-Software: VAX/VMS VNEWS 1.41 In article <1995Jan6.073436.13810@comp.bioz.unibas.ch>, doelz@comp.bioz.unibas.ch (Reinhard Doelz) writes... >David Mathog (mathog@seqvax.caltech.edu) wrote: >: It would be *really* nice if the folks who maintain and distribute >: databases would make it a bit easier to automate updates. >: etc. > >Comment 1: >The proposed stubs try to compensate the weakness of a transaction based >on a poll mechanism without query. Rather than the customer inquires in >detailed fashion, the current schema of FTP requires the FTP site to be >(1) fixed in file names (btw, what do you do with your software if a new >division appears) Actually, part of the purpose of stub.txt was to compensate for minor variances in file names/types/locations. If a new division appears it would have to be handled manually (the first time), same as it is now. >(2) preprepared for any request, be it day-by-day, >week-by-week, or other Well, yes, but the only valid "request" is "send me the description file". So in order to service that request all the FTP site needs is a current description file. Writing such a file might take 20 minutes the first time, but should only take seconds for an update. (Change the version number and date.) Part of the reason to use stub files is it would make it obvious to the FTP site maintainer when they have changed a file name, >, and (3) does not at all tackle the question what >to do with it. The proposed schema does not mention whether the target is >to update (1) formatted (which format? ), (2) unformatted or (3) incremental >data. In particular, the latter is most appropriate at wide area networks >to save badnwith, and raises management problems at the local site. Since WAN access is currently "free" we are not yet worrying about the economics of continuous incremental vs. "release" forms of update. While it is undoubtedly extremely wasteful of bandwidth, we replace the entire database at each release, rather than trying to incrementally upgrade it to the same state. You are right in that the stub files would be much more work for most types of incremental database updates. Of course, incremental updates are a big pain in their own right. > >Comment 2: >The proposed schema seems to imply a resource discovery based on static >listings. These are notoriously difficult to maintain and do not necessarily >offer a quality control issue (see below). Even if this were a possibility, >this implied that all sites referencing each other have the same policy of >'free for all' and do honor the same quality standards. Yeah, it would help if everybody could agree on a single format for the description files. History does not indicate that this is likely. > >Comment 3: >The major problem in sequence database updating is that the quality of >an update cannot be judged if you download it as file. Neither date nor >contents are sufficiently characterized in their format. A synchronisation >is required (or at least desirable) which allows to crosscheck the contents >of your local, adapted , formatted copy to the originally present data at >the provider. Versions and dates are nice but insufficient to characterize >a contents in incremental updates. > Quite right - there is no simple way to judge database quality. My (parasitic) strategy has been to let any database release "age" for a couple of weeks before downloading it. This has usually resulted in some other brave soul finding the problems in a particular release and the database provider subsequently fixing them. >Comment 4: >The proposed schema requires a considerable amount of coordination in >between providers. The resources for the update buisness are fairly low >as you, and many others, are neither prepared nor willing to pay for the >service you request. It was meant to be very cheap to implement on the server side - we're only talking 20-100 lines of text/major databases/site, and most of that will not change between releases. We dealt with coordination above. In closing - I'd happily live without the proposed files, so long as the database providers make more of an effort to keep filenames and paths the same between releases. Regards, David Mathog mathog@seqvax.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Fri Jan 06 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!spool.mu.edu!darwin.sura.net!maze.dpo.uab.edu!BCRF2!lefkowitz From: lefkowitz@orion.cmc.uab.edu (Elliot Lefkowitz) Newsgroups: bionet.software Subject: Re: GCG/SRS Date: Fri, 6 Jan 1995 17:31:57 UNDEFINED Organization: University of Alabama at Birmingham Lines: 33 Distribution: bionet Message-ID: References: <3ejhfv$pgr@mserv1.dl.ac.uk> NNTP-Posting-Host: bcrf2.microbio.uab.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #4] In article <3ejhfv$pgr@mserv1.dl.ac.uk> writes: >From: >Subject: GCG/SRS >Date: 6 Jan 1995 13:44:31 -0000 >In a recent weekly update of the EBI databank appeared the sequences of >yeast chromosome II and a long E. coli contig, both of them having more >than 350,000 bp. As you know, GCG will split them into 2 parts. >Now, the second part of the GCG formatted files contains NO accession >number. When SRS builds its indices from the GCG files, it is confused by >the absence of AC (at least that's what I understand) and it crashes. >Very very ennoying... Yes, we too have this problem when trying to index Genbank with SRS on our VAX GCG system. There are now three sequences in Genbank longer than 350,000 bases that cause this problem. I have been in contact with Thure Etzold, and he has been aware of the problem and has been working on a solution. As soon as he has made the necessary changes to the SRS code, I am sure that he will release the fix to the net. Thure has always been very diligent in responding to problems, and I would like to thank him for his work and the superb search utility, SRS. It is by far the best database searching utility I have used. Elliot Elliot Lefkowitz, Ph.D. University of Alabama at Birmingham Director, Biological Computing Resource Center Lefkowitz@orion.cmc.uab.edu From owner-software@net.bio.net Fri Jan 06 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!scripps.edu!scripps.edu!yagi2 From: yagi2@scripps.edu () Newsgroups: bionet.software Subject: Re: Problem with NCBI Gene Server???? Date: 6 Jan 1995 23:56:15 GMT Organization: The Scripps Research Institute, La Jolla, CA Lines: 23 Distribution: world Message-ID: <3eklav$bp1@riscsm.scripps.edu> Reply-To: yagi2@scripps.edu NNTP-Posting-Host: energy_pc.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In message , aj519@FreeNet.Carleton.CA (Robert W Beggs) writes: >Netters - > >Ive been trying to log onto the NCBI gene server >(retrieve@ncbi.nlm.nih.gov) to download some gene sequences> The body of >the message I've used has been: (stuff deleted) > >The server has refused to accept these arguments, and keeps sending me >error messages, or copies of the RETRIEVE help document...does anyone know >what I'm doing wrong? There was indeed a problem with the RETRIEVE server at NCBI. It was fixed yesterday. If you still get the error message back from the server, try informing the staff of the problem at retrieve-help@ncbi.nlm.nih.gov. But as far as I can tell, their program is working just fine now. Akemi Yagi yagi2@scripps.edu From owner-software@net.bio.net Fri Jan 06 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!comlab.ox.ac.uk!oxuniv!oxpath!birney Newsgroups: bionet.software Subject: VMS gurus.... Message-ID: <1995Jan7.191848.1@molbiol.ox.ac.uk> From: birney@molbiol.ox.ac.uk Date: 7 Jan 95 19:18:48 GMT Organization: Oxford University Molecular Biology Data Centre Nntp-Posting-Host: oxpath Nntp-Posting-User: birney Lines: 19 Hi... Is any out there a VAX guru...? Do you know how to get a listing of files in your current dir *inside* a C program in VMS (in a way in which the program can use it... system("DIR *.*") is no good)? For that matter has anyone got the best way of doing it in UNIX...I'm planning just to lift the code from K&R, but if someone has a better (ie more portable?) way of doing it then great. thanks alot ewan birney@molbiol.ox.ac.uk From owner-software@net.bio.net Fri Jan 06 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!lll-winken.llnl.gov!koriel!wnoc-sfc-news!wnoc-tyo-news!aist-nara!wnoc-kyo-news!kuis-news!jhlc475!e50501 From: e50501@sakura.kudpc.kyoto-u.ac.jp (Norio Mimura) Newsgroups: bionet.software Subject: Re: compiling RasMol 2.5 for HP-UX Date: 7 Jan 1995 12:00:22 GMT Organization: Faculty of Pharmaceutical Sciences Lines: 76 Distribution: world Message-ID: References: <3ekau9$4gd@vixen.cso.uiuc.edu> NNTP-Posting-Host: jhlc475.pharm.kyoto-u.ac.jp Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Newsreader: NewsWatcher-J 2.0b19J12 Hi Bill, In article <3ekau9$4gd@vixen.cso.uiuc.edu>, billh@lisboa.ks.uiuc.edu (William F. Humphrey) wrote: > Hi - > > Anybody managed to compile RasMol 2.5 for HP-UX 9.05? My rather quick > attempt to do this yielded the following problem: I could make RasMol 2.5.1 successfully on HP-UX 9.05 last year. :-) > > prospero:billh [40] % xmkmf Why didn't you use original Makefile? > mv Makefile Makefile.bak > imake -DUseInstalled -I/usr/local/lib/imake > > prospero:billh [41] % make > cc +O2 +Onolimit -Ae -I/usr/include/X11R5 -I/usr/local/include -DSYSV > -Dhpux -DRASMOLDIR=\"/usr/lib/X11R5 -L/usr/lib/X11R4/rasmol/\" -DEIGHTBIT -c > rasmol.c > cc +O2 +Onolimit -Ae -I/usr/include/X11R5 -I/usr/local/include -DSYSV > -Dhpux -DRASMOLDIR=\"/usr/lib/X11R5 -L/usr/lib/X11R4/rasmol/\" -DEIGHTBIT -c > molecule.c > cc +O2 +Onolimit -Ae -I/usr/include/X11R5 -I/usr/local/include -DSYSV > -Dhpux -DRASMOLDIR=\"/usr/lib/X11R5 -L/usr/lib/X11R4/rasmol/\" -DEIGHTBIT -c > abstree.c > cc +O2 +Onolimit -Ae -I/usr/include/X11R5 -I/usr/local/include -DSYSV > -Dhpux -DRASMOLDIR=\"/usr/lib/X11R5 -L/usr/lib/X11R4/rasmol/\" -DEIGHTBIT -c > command.c > cc: "command.c", line 761: error 1004: Unexpected end of line. > *** Error code 1 > > > If anyone has successfully done this, I would be very interested in and > appreciative for the information on how to finish the compilation. Thanks ... > A little changes were made, as % diff Makefile.in Makefile 1c1,2 < CC = gcc --- > CC = cc > #CC = gcc 12c13 < CFLAGS = -g -O2 -finline-functions --- > # CFLAGS = -g -O2 -finline-functions 31a33,35 > CFLAGS = -I/usr/include/X11R5 -Ae +O2 +Onolimit > LFLAGS = -L/usr/lib/X11R5 > and % diff rasmol.h.orig rasmol.h 41c41,42 < #define RASMOLDIR "/usr/local/lib/rasmol/" --- > /* #define RASMOLDIR "/usr/local/lib/rasmol/" */ > #define RASMOLDIR "/users/lib/" I suppose that your macro definition RASMOLDIR was not proper, because only command.c uses this def. Bye! -- Norio Mimura e50501@sakura.kudpc.kyoto-u.ac.jp /* Opinions expressed here are mine, not my faculty's. */ From owner-software@net.bio.net Fri Jan 06 22:00:00 1995 Path: biosci!rutgers!engr.orst.edu!gaia.ucs.orst.edu!slip45.UCS.ORST.EDU!bulsecod From: bulsecod@ucs.orst.edu (Dylan Bulseco) Newsgroups: bionet.software Subject: Re: Scatchard Analysis Software Date: Sat, 7 Jan 1995 10:36:20 GMT Organization: Dept. of Biochemistry, Oregon State University Lines: 36 Distribution: world Message-ID: References: <3ehenh$fbr@lastactionhero.rs.itd.umich.edu> NNTP-Posting-Host: slip45.ucs.orst.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] In article <3ehenh$fbr@lastactionhero.rs.itd.umich.edu> Chris Beecher writes: >From: Chris Beecher >Subject: Scatchard Analysis Software >Date: 5 Jan 1995 18:45:05 GMT >I am looking for PC or Mac software that can do a Scatchard analysis for >at least one-site ligand binding experiments. >I am already familair with Ligand and it barely gets by, can anyone >recommend something better without spending an arm and a leg? >chris beecher >Univ of Mich If you want a commercial package with built in routines (for Windows), try Prism (from GraphPad). It will has built in eqns for one and two site direct binding experiments (saturation plots) as well as competition/displacement binding experiments. If you need to enter your own equations (ie: to go to 3 sites etc.), Prism may not be ideal. (and yes...non-linear curve fits are the way to go...forget about scatchard analysis). Of course, GraphPad also sells DOS software that does similar things (called GraphPad/InPlot?). A general data analysis package (also Windows), is Origin (from Microcal). None of the data binding routines are built in (although the logistic eqn is...for dose response experiments), but it is really easy to enter your own equations. Or, for a DOS package, SigmaPlot works great (no built in eqns except logistic, but great for user entered). For shareware type packages, 'Techplot' (I think that is what it is called) is still floating around out there (perhaps on a SIMTEL site). This appears to be a pre-release of PSI Plot (or the name was changed or something). I used it for awhile, and it seemed to work ok, but had a few minor problems. Anyway...look for a package with non-linear curve fitting, with both built in equations, and the ability to enter your own. From owner-software@net.bio.net Fri Jan 06 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!library.ucla.edu!news.mic.ucla.edu!usenet From: Xiao-Jun Ma Newsgroups: bionet.software Subject: Coiled-coil prediction Date: 7 Jan 1995 04:47:07 GMT Organization: UCLA Microcomputer Support Office Lines: 1 Message-ID: <3el6cb$rs1@news.mic.ucla.edu> NNTP-Posting-Host: modem0-g.lifesci.ucla.edu Is there mac (or other platforms) programs for predicting coiled-coi structures for my newly sequenced proteins? From owner-software@net.bio.net Sat Jan 07 22:00:00 1995 Newsgroups: bionet.software,bionet.software.gcg Path: biosci!agate!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: Re: GCG/SRS Message-ID: Sender: news@ebi.ac.uk (Mr news) Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] References: <3ejhfv$pgr@mserv1.dl.ac.uk> Distribution: bionet Date: Fri, 6 Jan 1995 14:10:57 GMT Lines: 52 Xref: biosci bionet.software:10584 bionet.software.gcg:901 risler@cgmvax.cgm.cnrs-gif.fr wrote: : Hello netters, [...] : In a recent weekly update of the EBI databank appeared the sequences of : yeast chromosome II and a long E. coli contig, both of them having more : than 350,000 bp. As you know, GCG will split them into 2 parts. : Now, the second part of the GCG formatted files contains NO accession : number. When SRS builds its indices from the GCG files, it is confused by : the absence of AC (at least that's what I understand) and it crashes. : Very very ennoying... As far as I can see from the SRS code, the AC line is required. Not an easy way round. (But I could be wrong :-) ) : Have you any idea? Can somebody help me? I'm somewhat reluctant to simply : remove these sequences from the flat file, which in any case could be only : a very temporary fix... An easier way would be to add a dummy accession line to these sequences. We could ask in bionet.software.gcg if the reformatting of GCG could be altered to add this AC line. : Thank you : Jean-Loup : --------------------------------------------------------------------- : Jean-Loup Risler Tel: (33 1) 69 82 31 34 : CNRS Fax: (33 1) 69 07 49 73 : Centre de Genetique Moleculaire Email: risler@cgmvax.cgm.cnrs-gif.fr : 91198 Gif sur Yvette Cedex France : --------------------------------------------------------------------- Jeroen -- ====================================================================== . O . Jeroen Coppieters . O O o O . Software Support O O O O *o O O Jeroen.Coppieters@ebi.ac.uk O O O O( *o )O O ++44 1223 494422 )O O O O o* O O( O O O O( o* )O O )O O O O *o O O( EMBL Outstation EBI O O O O( *o )O O (European Bioinformatics Institute) )O @ O O o* O O( Hinxton Hall O O O( o* )O(' Hinxton ` O( *o O ' Cambridge CB10 1RQ ` O ' UK http://www.ebi.ac.uk ====================================================================== From owner-software@net.bio.net Sat Jan 07 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.software Subject: Re: cDNA extraction Date: 8 Jan 1995 22:09:32 -0000 Lines: 32 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3epnqs$ob8@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk R. Doelz writes: > >SRS can extract CDS from entire sequende databases and combine, map, filter >with whatever database or database query you want (currently, > 50 databases. >Check out http://www.ch.embnet.org/srs/status.html for reference). > Reinhardt, this is quite true! However: is SRS able to use the JOIN feature? Last time I used it for this purpose, SRS extracted correctly all the CDS but created one entry for each CDS. As I understand it, the problem here is to JOIN all the exons of one given gene into one single sequence ("cDNA"). Hence my previous answer about ACNUC. If SRS can do this, I would be VERY interested to learn the trick! Regards, Jean-Loup --------------------------------------------------------------------- Jean-Loup Risler Tel: (33 1) 69 82 31 34 CNRS Fax: (33 1) 69 07 49 73 Centre de Genetique Moleculaire Email: risler@cgmvax.cgm.cnrs-gif.fr 91198 Gif sur Yvette Cedex France --------------------------------------------------------------------- From owner-software@net.bio.net Sat Jan 07 22:00:00 1995 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.software Subject: Re: cDNA extraction from databases Date: 8 Jan 1995 21:47:49 -0000 Lines: 46 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3epmi5$n5j@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk Steve Taylor wrote: > >I seem to remember some time ago I saw some freeware which allowed you >to extract relevant information from EMBL or Genbank database entry >feature tables. > >I would like to be able to pull out full length cDNAs from a collection of >database entries and don't want to have to examine every feature table >by hand to find where the exons are ! Anything that does >this sort of operation would be useful. > ACNUC will do this easily, provided that the feature table in EMBL or Genbank is up to date and contains the "JOIN" field (unfortunately, many many sequences in EMBL have not been updated. I don't know about Genbank). to get ACNUC (VMS or Unix), ftp to biom3.univ-lyon1.fr If you want more details, send a mail to the author (Manolo Gouy) at: mgouy@biomserv.univ-lyon1.fr Good luck, Jean-Loup --------------------------------------------------------------------- Jean-Loup Ris