From owner-software@net.bio.net Sun May 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!caen!batcomputer!ghost.dsi.unimi.it!univ-lyon1.fr!news From: duret@evoserv.univ-lyon1.fr (Laurent Duret) Newsgroups: bionet.software Subject: Re: non-specific primers for human genomic seq Date: 2 May 1994 06:34:38 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 22 Distribution: world Message-ID: <2q26tu$7sr@cismsun.univ-lyon1.fr> References: <2prd2f$kgj@csi0.csi.uottawa.ca> Reply-To: duret@evoserv.univ-lyon1.fr NNTP-Posting-Host: evoserv.univ-lyon1.fr In article kgj@csi0.csi.uottawa.ca, sbaird@mgcheo.med.uottawa.ca (Stephen Baird) writes: > I'm looking for ideas or references on non-specific primers to > amplify human genomic sequences. I'd like to amplify small pieces > (around 200-500bp) preferably without repetitive elements and > preferentially amplify human sequences over any contaminating > sequence from bacteria. When doing database searches with small > pieces of human genomic sequence like 100-150bp, more often than > not the top scores are all human sequences even if the scores are > very low. Just be careful. Human sequences represent about 20% of all GenBank sequences, while E. coli sequences represent only 3%. So, even with a random sequence, you may expect that similarity search programs will find a human sequence much more often than one from any other species. However, this does not exclude the possibility of species-specific sequences. Laurent Duret From owner-software@net.bio.net Mon May 02 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Germany.EU.net!nntp.gmd.de!dearn!barilvm!vms.huji.ac.il!agri.huji.ac.il!dvorah Newsgroups: bionet.software Subject: gel analysis and databases Message-ID: <3MAY199412325492@agri.huji.ac.il> From: dvorah@agri.huji.ac.il (DVORAH ART) Date: 3 May 1994 12:32 GMT Distribution: world Organization: The Hebrew University of Jerusalem Keywords: 1-d gel, lane, database, pattern matching Nntp-Posting-Host: agri.huji.ac.il News-Software: VAX/VMS VNEWS 1.41 Lines: 37 One of our faculty members has just purchased a gel documenting system (ie. a light table, a camera, a printer and an "imaging processor" that creates tiff files.) He wants to purchase software for analysis of his 1-D gels, and wants to extract the position and molecular weight information from a lane, store it (as a lane?)in a database, and use the database to tell him if he's seen a particular pattern before. He is accustomed to using IBM-PC clones, but he also has at his disposal (if necessary) a VAX running VMS & a Silicon Graphics Indy. I have some names of PC, Mac, and Unix based gel analysis software, but I'd like to get a list of software that "you out there" are aware of, have used, your experiences with it, and contact people. (For both commercial and academic software). I am particularly in the dark about using database software for this purpose, and about how pattern matching is done. I have before me a brochure for UVP's GelMatch, but the brochure doesn't give info about how comparisons are done. If anyone has references to articles on the subject (in addition to names of software and contacts) I'd be happy to get them. Please send info directly for me, and if the info is useful, I'll reorganize and repost. Thanks, Deborah Art-Weisman Computer Center - Faculty of Agriculture Hebrew University of Jerusalem dvorah@agri.huji.ac.il From owner-software@net.bio.net Mon May 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!nntp.uio.no!NewsWatcher!user From: olam@radium.uio.no (Ola Myklebost) Newsgroups: bionet.software Subject: Re: Networking Help Request - MD Phospherimager Followup-To: bionet.software Date: Tue, 03 May 1994 09:51:15 +0100 Organization: Inst for Cancer Research, Oslo Lines: 22 Distribution: world Message-ID: References: <3388.2dbba83d@mbcl.rutgers.edu> <2pond4$nrh@netnews.upenn.edu> NNTP-Posting-Host: pcdnr05.uio.no Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit > In article <3388.2dbba83d@mbcl.rutgers.edu>, harrison@mbcl.rutgers.edu writes: > |> > |> Hello, > |> > |> I'm am trying to get a Molecular Dynamics Phospherimager on > |> the net. I have a NE200 Ethernet Adaptor, LocalTalk and > |> the necessary HW and IP address. If anyone has had sucess > |> doing this, could you please tell me what packet driver, > |> comm SW you used? The protocol would be appreciated too. It is a bit difficult to find free memory space for the ethernet drivers. I successfully use IRQ3, I/O 250, MEM disabled (With PC-NFS, but I also tried timbuktu/Pnonenet (Ethertalk) successfully) -- Ola Myklebost Email ola.myklebost@labmed.uio.no Dept of Tumor Biology Inst for Cancer Research Tel +47-2293-4299 The Norwegian Radium Hospital Fax +47-2252-2421 N-0310 OSLO, Norway From owner-software@net.bio.net Mon May 02 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!pipex!sunic!news.funet.fi!ousrvr.oulu.fi!sun3!ojtv From: ojtv@sun3.oulu.fi (Olli Vuolteenaho) Subject: DNA Strider, Fax number? Message-ID: <1994May3.091242.13641@ousrvr.oulu.fi> Sender: news@ousrvr.oulu.fi Organization: University of Oulu, Department of Physiology X-Newsreader: TIN [version 1.2 PL1] Date: Tue, 3 May 1994 09:12:42 GMT Lines: 8 Does anyone know the fax number (or email address) of the distributors of DNA Strider (Christian Marck, Gif-Sur-Yvette, France (?))? Thank you Olli olli.vuolteenaho@oulu.fi From owner-software@net.bio.net Mon May 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!gatech!swrinde!ihnp4.ucsd.edu!library.ucla.edu!csulb.edu!kmiles From: kmiles@csulb.edu (Kevin Miles) Newsgroups: bionet.software Subject: looking for ADAM software Date: 3 May 1994 00:36:53 GMT Organization: Cal State Long Beach Lines: 9 Message-ID: <2q46b5$77q@garuda.csulb.edu> NNTP-Posting-Host: beach.csulb.edu X-Newsreader: TIN [version 1.2 PL2] Recently saw on CNN report on a software package called ADAM. Did not have opportunity to get information on accessing program. I do know that the creator is Art English at Emory Medical School. Any help would be appriciated. Kevin A. Miles Kmiles.beach.csulb.edu From owner-software@net.bio.net Mon May 02 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!mozart.amil.jhu.edu!blaze.cs.jhu.edu!jhunix.hcf.jhu.edu!NewsWatcher!user From: Lys@jhuigf.bitnet (Lys Guilbride) Newsgroups: bionet.software Subject: ENTREZ Followup-To: bionet.software Date: 3 May 1994 15:00:57 GMT Organization: Johns Hopkins Lines: 4 Message-ID: NNTP-Posting-Host: 128.220.56.197 Anyone who has idea about ENTREZ, please send information to me. I would like to know what it does and how I could obtain a copy of the program. Please reply to the news group or send an E-Mail to me. The address is lys@jhuigf.bitnet. Thank you. Lys From owner-software@net.bio.net Mon May 02 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.cac.psu.edu!psuvm!imeg Organization: Penn State University Date: Tue, 3 May 1994 17:55:17 EDT From: Sudhir Kumar Message-ID: <94123.175517IMEG@psuvm.psu.edu> Newsgroups: bionet.software,bionet.molbio.evolution Subject: MEGA: Order info repost on request Lines: 286 Xref: biosci bionet.software:8080 bionet.molbio.evolution:1668 This document contains many pages, including 1. Cover letter 2. Order form (We no longer accept purchase orders) 3. Hardware and software requirements 4. Program upgrade policy 5. Functions in MEGA MEGA version 1.0, 1.01 September, 1993 To whom it may concern: A computer software called MEGA: Molecular Evolutionary Genetics Analysis has been developed. This software is for facilitating statistical studies of molecular evolution by using IBM compatible personal computers. It contains various methods of estimating evolutionary distances and three different methods of phylogenetic inference (UPGMA, neighbor-joining, and maximum parsimony) with either a standard-error test or a bootstrap test of topological differences. For the maximum parsimony method, new algorithms of the branch-and-bound and heuristic searches are implemented. MEGA also computes basic statistical quantities such as nucleotide and amino acid frequencies, transition/transversion bias, codon usage frequencies, number of variable sites, etc. In addition, advance on- screen sequence data and phylogenetic tree editors are included. Integrated and interactive designs, on-line context-sensitive helps, text-file editor, and other unique features make it easy to use MEGA. MEGA version 1.0 is distributed with a nominal fee to defray the cost of producing the user manual (140 pp.) and diskettes, and the mailing and handling expenses (see enclosed order form). However, for anyone who is unable to pay the fee for some reason, it will be provided free of charge after receiving a letter explaining the circumstances. MEGA will not be sent by electronic-mail because the accompanying manual cannot be included in this case. Technical questions and other inquires about MEGA should be directed to the senior author of the software. Please include your electronic-mail address, if any. Sincerely yours, Sudhir Kumar Koichiro Tamura Masatoshi Nei Telephone: (814) 863-7334 FAX: (814) 863-7336 E-mail: imeg@psuvm, imeg@psuvm.psu.edu MEGA ORDER FORM Cost* ----------------------------------------------------------------- Program No Charge User manual, diskette, shipping, and handling $ 15.00 For shipment outside North America add $10.00 _________ (We will use first class airmail) TOTAL _________ ----------------------------------------------------------------- * This cost can be waived if the circumstances for the inability to pay (e.g., lack of hard currencies in some countries) are explained. Diskette type desired: Please specify: [ ] 3.5" Diskette (1.44MB) [ ] DOS Version ...... [ ] 5.25" Diskette (1.2MB) [ ] Computer system... [ ] other (specify).... [ ] Do you use windows? Yes/No All orders must be prepaid in U.S. dollars. Return this form together with a check or money order payable to Penn State University at the following address. Purchase orders will not be accepted. Joyce White Institute of Molecular Evolutionary Genetics The Pennsylvania State University 328 Mueller Laboratory University Park, PA 16802 USA Telephone: (814)-863-7334 Fax: (814)-863-7336 E-mail: IMEG@PSUVM.PSU.edu, IMEG@PSUVM About the user: Name: ____________________________________________ Address: ____________________________________________ ____________________________________________ ____________________________________________ Telephone: _____________________ Fax: _________________ E-Mail: ____________________________________________ --------Hardware and Software------ IBM and IBM-compatible PCs, XTs, ATs, etc. Color/monochrome monitors. 640KB RAM memory. DOS version 3.3 or later. Hard disk with 2MB free. No extended or expanded memory required. No graphics adapters required. No math-chip required. Supports the keyboard as well as the mouse (not essential). ------- Program upgrade policy ---- Since MEGA is in its first version, there may be many software bugs in the program. We are considering to provide registered users a version where bugs reported in version 1.0 and 1.01 will be fixed. As you may notice from the order form, we are just trying to recover the cost of distributing MEGA only. So we are not in a position to provide many upgrades. In any case, we do not plan to include new methods in MEGA soon (for at least one year), and therefore the questions about upgrades may not be so pressing at this moment. -------Functions in MEGA------- Input Input data: DNA sequences RNA sequences Amino acid sequences Distance matrices Input formats: Interleaved sequences Non-interleaved sequences Upper-triangular distance matrix Lower-triangular distance matrix Choice of: Alignment gap symbol Missing-information site symbol Identical site symbol In-memory data editing features Selection: Desired OTUs Domains of sequences Individual sites and codons Codon positions Exclude/include missing information sites Exclude/include alignment gap sites Edit OTU labels Restore OTU labels Sequence data presentation Highlight: Variable sites Parsimony-informative sites Two-fold redundant sites Four-fold redundant sites Translate: Translation of nucleotide sequences into amino acid sequences Output: Formats: MEGA PAUP PHYLIP Publication Data subsets: Only variable sites Only parsimony-informative sites Amino acid sequences translated Codon positions Sequence statistics: Nucleotide and amino acid frequencies Nucleotide pair frequencies in pairwise comparisons Insertion-deletion frequencies Codon usage frequencies Relative synonymous codon usage (RSCU) values Variable sites in overlapping segments Variable sites in nonoverlapping segments Distance estimation Nucleotide substitutions Quantities: Number of nucleotide differences Nucleotide substitutions Transitional substitutions Transversional substitutions Transition/transversion ratio Distance measures: p-distance Jukes-Cantor distance Kimura 2-parameter distance Tajima-Nei distance Tamura distance Tamura-Nei distance Gamma distances Jukes-Cantor model Kimura 2-parameter model Tamura-Nei model Synonymous-nonsynonymous substitutions Genetic code tables: "Universal" Mammalian mitochondrial Drosophila mitochondrial Yeast mitochondrial Computation: Synonymous substitutions Nonsynonymous substitutions Average distances for all pairwise comparisons and standard errors Amino acid substitutions Distance measurers: Number of amino acid differences p-distance Poisson-correction distance Gamma distance Distance output: Control on: Page size Precision for distance output Distance q standard error formats Tree building and test Methods: Neighbor-joining (NJ) UPGMA Maximum parsimony (MP): Branch-and-bound search Heuristic search Statistical Tests: Bootstrap test: Neighbor-joining UPGMA Branch length test: Neighbor-joining Phylogeny editing: Tree re-rooting Swapping and flipping branches Consensus tree Condensed tree Phylogeny printing: Various printers Multiple page printouts Choice of fonts Choice of orientation Choice of page size Tree preview General functions File browsing File editing Exiting to DOS temporarily Context-sensitive Helps Error messages From owner-software@net.bio.net Mon May 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!cornell!batcomputer!ghost.dsi.unimi.it!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!sun.rediris.es!news.uam.es!samba.cnb.uam.es!lpezzi From: lpezzi@samba.cnb.uam.es Newsgroups: bionet.software Subject: GeneWorks vs. DNAStar Date: 3 May 94 18:13:21 WET Organization: C.N.Biotecnologia, CSIC Lines: 10 Message-ID: <1994May3.181321.1@samba.cnb.uam.es> NNTP-Posting-Host: samba.cnb.uam.es We are considering the purchase of GeneWorks of DNAStar for our institution. Any comments on the relative merits of both programs ? Thanks in advance Luis Pezzi Centro Nacional de Biotecnologia Madrid. Spain From owner-software@net.bio.net Mon May 02 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!torn!nott!uotcsi2!usenet From: misrael@grdb.csi.uottawa.ca (Mark Israel) Newsgroups: bionet.software Subject: Re: GOOD SEQUENCE PROGRAM Date: 3 May 1994 16:46:30 GMT Organization: Dept. of Computer Science, University of Ottawa Lines: 36 Message-ID: <2q5v56$7g3@csi0.csi.uottawa.ca> References: <2q5psr$5f2@netnews.upenn.edu> NNTP-Posting-Host: grdb.csi.uottawa.ca In article <2q5psr$5f2@netnews.upenn.edu>, Sean David Moore writes: > I am looking for the name and/or location of the best sequence alignment > program. [...] > > Is there even such a thing.? > > No responses as of the fifth post of this message were received except to > ask for the response. Well, the following were described as "optimal"; so maybe they're the best. Just a wild guess. (This was posted only a month ago. Maybe it's time to start an FAQ file for this newsgroup.) misrael@csi.uottawa.ca Mark Israel --------------------------------------------------------------------------- Newsgroups: bionet.software Subject: Re: Software for sequence alignment? From: wrp@dayhoff.med.Virginia.EDU (William R. Pearson) Organization: University of Virginia Date: Thu, 31 Mar 1994 14:28:18 GMT Message-ID: [...] The "align" program in the FASTA package (available from "virginia.EDU" in "pub/fasta/fasta17.shar.Z") will produce optimal global alignment with gaps for DNA and protein sequences. It aligns only two sequences at once. The only genuine optimal alignment program for multiple sequences that I am aware of is "msa" (Lipman, Altschul, and Kececioglu, (1989) PNAS 86:4412-4415) which is available from ncbi.nlm.nih.gov. Bill Pearson From owner-software@net.bio.net Mon May 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!europa.eng.gtefsd.com!emory!news-feed-2.peachnet.edu!news-feed-1.peachnet.edu!news.duke.edu!godot.cc.duq.edu!toads.pgh.pa.us!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!mail.sas.upenn.edu!smoore From: smoore@mail.sas.upenn.edu (Sean David Moore) Newsgroups: bionet.software Subject: GOOD SEQUENCE PROGRAM Date: 3 May 1994 15:16:43 GMT Organization: University of Pennsylvania Lines: 20 Message-ID: <2q5psr$5f2@netnews.upenn.edu> NNTP-Posting-Host: mail.sas.upenn.edu X-Newsreader: TIN [version 1.2 PL2-upenn1.1] If anyone reads this message base anymore: I am looking for the name and/or location of the best sequence alignment program. Most of the modern programs do many things (i.e. primer analysis multi-reference searches, blast searches etc.) I would like it for IBM, preferably Windows. Is there even such a thing.? No responses as of the fifth post of this message were received except to ask for the response. SEAN MOORE smoore@sas.upenn.edu baldy@brahms.udel.edu TATABOX@aol.com From owner-software@net.bio.net Mon May 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!gatech!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!news.amherst.edu!not-for-mail From: rmsmith@unix.amherst.edu (Robert M. Smith) Newsgroups: bionet.software Subject: PC Protein _Viewing_. Date: 2 May 1994 20:33:18 -0400 Organization: Amherst College, Amherst MA, USA Lines: 17 Message-ID: <2q464e$9s2@amhux3.amherst.edu> NNTP-Posting-Host: amhux3.amherst.edu X-Newsreader: TIN [version 1.2 PL0] I am interested in acquiring protein viewing software for a PC. I use an SGI Iris with Quanta and CHARMm at lab but would like to be able to view certain results graphically from home. Ideally, I would like something that would allow me to display color SVGA stick figures, rotate them, and even display van der Waals radii (as dots, not solids). High resolution and the ability to rotate are essential as is low cost (<$200). Any assistance is greatly appreciated. Thanks. Rob ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Rob Smith rmsmith@amhux3.amherst.edu Department of Chemistry, a Program in Molecular and Cellular Biology Amherst College, n University of Massachusetts, Amherst, MA 01002 d Amherst, MA 01003 Phone: (413) 542-2558 FAX: (413) 542-2558 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-software@net.bio.net Mon May 02 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: plxigpg@vax.ccc.nottingham.ac.uk Newsgroups: bionet.software Subject: Tektronix graphics on Mac Date: 3 May 1994 11:10:38 +0100 Lines: 11 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2q57uu$l08@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk Dear all, Can anyone tell me how to increase the size of a Tektronix graphics window on a Mac. I'm using it for GCG graphics - but a lot of them do not fit onto the screen. Thanks in advance. Ian plxigpg@ccc.nottingham.ac.uk From owner-software@net.bio.net Tue May 03 23:00:00 1994 Path: biosci!headwall.Stanford.EDU!morrow.stanford.edu!morrow.stanford.edu!not-for-mail From: HF.JSL@forsythe.stanford.edu (Joseph Lipsick) Newsgroups: bionet.software Subject: Re: ENTREZ Date: 4 May 1994 16:38:38 -0700 Organization: Stanford University Lines: 17 Sender: news@morrow.stanford.edu Distribution: usa Message-ID: <2q9blu$78d@morrow.stanford.edu> NNTP-Posting-Host: morrow.stanford.edu I heartily recommend ENTREZ as well. It contains both DNA and protein seq. databases, relevant Medline references, and a nice software interface for searching. It is also the best software bargain I've seen-- updates regularly on CD-ROM at a minimal cost. It has replaced much of my e-mail searching of Genbank excepting for the latest "updated" sequences since the last release of ENTREZ. Another amazing bargain from the folks at NCBI is the MACAW program for finding local sequence homologies. You can spend a lot more money (especially since MACAW is free, or at least already paid for by your tax dollars), and won't do better elsewhere. Joe Lipsick P.S. The US government publications office which handles ENTREZ distribution is not the most user-friendly organization. Be persistent. Fortunately, once you're on the mailing list it's easy to stay on. From owner-software@net.bio.net Tue May 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!nctuccca.edu.tw!news.cc.nctu.edu.tw!cc.ntnu.edu.tw!snow!cnchu From: cnchu@ice.ntnu.edu.tw (Chu Chi-Nung) Subject: Processor Wanted Message-ID: <1994May4.080551.7336@cc.ntnu.edu.tw> Sender: news@cc.ntnu.edu.tw Nntp-Posting-Host: snow.ice.ntnu.edu.tw Organization: NTNU, Taiwan, R.O.C. X-Newsreader: TIN [version 1.2 PL2] Date: Wed, 4 May 1994 08:05:51 GMT Lines: 31 China Junior College of Industrial and Commercial Management, one of the most brilliant junior colleges in Northern Taiwan, is sincerely inviting high caliber applicants to join ourgrowing family. We have the vacacies for Assitant and Associate Professors in the following Department: International Trade Business Administration Finance and Taxation Accounting Management of Information Science * Applicants should be a business major with specialties in International Trade, Business Administration, Finance and Taxation, Accountion, Finance, Economics, or Management of Information Science. * Ph. D. preferred. * Teachig experience desired. * Handsome benifit. Salary matchies that of public university. * Special research or moving allowance is also granted. Please, contact usand send your resume as quickly as possible by the following means: * E-Mail * Tel: 886-2-935-1907 * FAX: 886-2-931-5132 * Add: Josephine Shang-Kuan Su, Chairperson of the Board China Junior College of Industrial and Commercial Management No.56, Section 3, Hsing-Lung Road, Wen Shan District, Taipei 117, Taiwan, R. O. C. From owner-software@net.bio.net Tue May 03 23:00:00 1994 Path: biosci!agate!library.ucla.edu!csulb.edu!nic-nac.CSU.net!usc!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!mozart.amil.jhu.edu!blaze.cs.jhu.edu!jhunix.hcf.jhu.edu!NewsWatcher!user From: djackson@welchlink.welch.jhu.edu (Donald G. Jackson) Newsgroups: bionet.software Subject: Re: ENTREZ Followup-To: bionet.software Date: 4 May 1994 13:28:11 GMT Organization: The Johns Hopkins University School of Medicine Lines: 31 Message-ID: References: NNTP-Posting-Host: 128.220.56.48 In article , Lys@jhuigf.bitnet (Lys Guilbride) wrote: > Anyone who has idea about ENTREZ, please send information to me. > I would like to know what it does and how I could obtain a copy of the > program... I thought other folks might be interested in this too so I'm posting my reply. We've been using entrez for a couple of years now and LOVE it. Basically, entrez is a database of sequences and their related references. All of the linkages in the database are already established, so your computer doesn't have to go chugging through the whole thing every time you go looking for a paper. You can use it to search protein or nucleotide sequence databases for an entry (not for sequence alignments a la blast or fasta) or a subset of the medline database. It has some neat features like "neighboring" (finding papers related to the selected paper) and "lookup" (find the reference for this sequence and show me the abstract or vice versa). Entrez is available in two ways: on CD-ROM from the U. S. Government Printing Office (about $72/year for 6 sets of 2 CD's-cheaper than cutouts at a record store!) or over the internet as "network entrez". Network entrez is a front end that connects with a server at NCBI (sort of like gopher, for those familiar with it) which is where the database is located. It's free and you don't need a CD drive. For information on how to get it, try contacting entrez@ncbi.nlm.nih.gov or call (301) 496-2475. One advantage that the CD version has, though: MacVector (and possibly other sequence analysis programs) can "browse" this database and retrieve sequences as MacVector files all ready to play with. This doesn't work with the network version. In summary, It's a pretty good program at a great price! From owner-software@net.bio.net Tue May 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!library.ucla.edu!psgrain!nntp.cs.ubc.ca!utcsri!newsflash.concordia.ca!sifon!athena.ulaval.ca!cube.bcm.ulaval.ca!user From: pagilbert@cti.ulaval.ca (Philippe-Alexandre Gilbert) Subject: VMS compilation of FASTA17 Message-ID: Followup-To: bionet.software Sender: news@athena.ulaval.ca Nntp-Posting-Host: cube.bcm.ulaval.ca Organization: Universite Laval Date: Tue, 3 May 1994 17:56:59 GMT Lines: 14 Dear BioNet users, We are running on a VAX 6410 with VMS V5.5. We would like to compile the version of FASTA17 from William R. Pearson. Did soemone experienced this problem and could send us a copy of a makefile for VMS. The VMS makefile included with the package does not work for version 16 and 17. Thank you for your help. -- Philippe-Alexandre Gilbert tel: (418)-656-2964 Centre de Traitement de l'Information e-mail: pagilbert@cti.ulaval.ca Departement de Biochimie Quebec, Canada From owner-software@net.bio.net Tue May 03 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!howland.reston.ans.net!torn!nott!uotcsi2!mgcheo.med.uottawa.ca!sbaird From: sbaird@mgcheo.med.uottawa.ca (Stephen Baird) Newsgroups: bionet.software Subject: Re: non-specific primers for human genomic seq Date: 4 May 1994 00:35:02 GMT Organization: Department of Computer Science, University of Ottawa Lines: 40 Distribution: world Message-ID: <2q6qjm$eea@csi0.csi.uottawa.ca> References: <2q26tu$7sr@cismsun.univ-lyon1.fr> NNTP-Posting-Host: mgcheo.med.uottawa.ca X-Newsreader: TIN [version 1.1 PL8] Laurent Duret (duret@evoserv.univ-lyon1.fr) wrote: : In article sbaird@mgcheo.med.uottawa.ca (Stephen Baird) writes: : > I'm looking for ideas or references on non-specific primers to : > amplify human genomic sequences. I'd like to amplify small pieces : > (around 200-500bp) preferably without repetitive elements and : > preferentially amplify human sequences over any contaminating : > sequence from bacteria. When doing database searches with small : > pieces of human genomic sequence like 100-150bp, more often than : > not the top scores are all human sequences even if the scores are : > very low. : Just be careful. Human sequences represent about 20% of all GenBank sequences, while : E. coli sequences represent only 3%. : So, even with a random sequence, you may expect that similarity search programs will : find a human sequence much more often than one from any other species. : However, this does not exclude the possibility of species-specific sequences. : Laurent Duret I`ve found the same results with both sequences from bacterial contamination and drosophila clones. With bacterial sequences the search results are dominated with bacteria and with drosophilia sequence queries, the results are mostly drosophila. There may have been species-specific sequences in many of these sequences. |--------------------------------------------------------------------| | Stephen Baird sbaird@mgcheo.med.uottawa.ca | | Molecular Genetics tel: 613-738-3925 | | Children's Hospital of Eastern Ontario fax: 613-738-4833 | | 415 Smyth Rd. | | Ottawa, Ontario | | Canada | | K1H 8M8 | |--------------------------------------------------------------------| From owner-software@net.bio.net Tue May 03 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!psgrain!nntp.cs.ubc.ca!unixg.ubc.ca!quartz.ucs.ualberta.ca!max From: max@mycroft.mmid.ualberta.ca (Max Cummings) Newsgroups: bionet.software Subject: Scrutineer (was junk) Date: 4 May 1994 22:16:26 GMT Organization: Department of Medical Microbiology and Infectious Diseases, University of Alberta Lines: 18 Message-ID: <2q96rq$gf8@quartz.ucs.ualberta.ca> NNTP-Posting-Host: clouseau.mmid.ualberta.ca X-Newsreader: TIN [version 1.2 PL2] I am looking for a unix version (to run on an SGI Indy) of a program called Scrutineer which calculates the amino acid composition of proteins in databases such as PIR and SWISS-PROT. The program was supposed to be (according to Anal. Biochem. 198:330(1991)) at EMBL-Heidelberg.de under unix software but I could only see a vax version. Anybody know where this beast is? Thanks, -- Max Cummings, MMID, 1-41 Medical Sciences Bldg., University of Alberta, Edmonton, Alberta, CANADA, T6G 2H7 Tel: 403-492-7581 or 4696; FAX: 403-492-7521 max@clouseau.mmid.ualberta.ca From owner-software@net.bio.net Tue May 03 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!psgrain!nntp.cs.ubc.ca!unixg.ubc.ca!quartz.ucs.ualberta.ca!max From: max@mycroft.mmid.ualberta.ca (Max Cummings) Newsgroups: bionet.software Subject: junk Date: 4 May 1994 22:07:21 GMT Organization: Department of Medical Microbiology and Infectious Diseases, University of Alberta Lines: 16 Message-ID: <2q96ap$gde@quartz.ucs.ualberta.ca> NNTP-Posting-Host: clouseau.mmid.ualberta.ca X-Newsreader: TIN [version 1.2 PL2] I am looking for a unix version (to run on an SGI Indy) of a program called Scrutineer which calculates the amino acid composition of proteins in databases such as PIR and SWISS-PROT. The program was supposed to be (according to Anal. Biochem. 198:330(1991)) at EMBL-Heidelberg.de under unix software but I could only see a vax version. Anybody know where this beast is Thanks, -- Max Cummings, MMID, 1-41 Medical Sciences Bldg., University of Alberta, Edmonton, Alberta, CANADA, T6G 2H7 Tel: 403-492-7581 or 4696; FAX: 403-492-7521 max@clouseau.mmid.ualberta.ca From owner-software@net.bio.net Tue May 03 23:00:00 1994 Path: biosci!ciens.ula.ve!alejo From: alejo@ciens.ula.ve (ALEJANDRO MUJICA) Newsgroups: bionet.software Subject: Re: PC Protein _Viewing_. Date: 4 May 1994 11:24:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 84 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9405041823.AA02232@merlin.ciens.ula.ve> NNTP-Posting-Host: net.bio.net Rob Smith writes: ----- Begin Included Message ----- I am interested in acquiring protein viewing software for a PC. I use an SGI Iris with Quanta and CHARMm at lab but would like to be able to view certain results graphically from home. Ideally, I would like something that would allow me to display color SVGA stick figures, rotate them, and even display van der Waals radii (as dots, not solids). High resolution and the ability to rotate are essential as is low cost (<$200). Any assistance is greatly appreciated. Thanks. ----- End Included Message ----- Rob: Hypercube's HyperChem is not so cheap, but it's pretty good for constructing proteins and nucleic acids. It also perfoms some complex chemical calculations and it reads files from the Brookhaven Protein Data Bank. Realease 3 runs for both PCs and SGIs. Enclosed, you'll find the anounce of the last release from hypercube. see you Alejandro ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Alejandro Mujica e-mail: alejo@ula.ve SUMA Facultad de Ciencias Universidad de Los Andes Tel: (58 74) 401284 Merida - Venezuela Fax: (58 74) 401286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ----- Begin Included Message ----- From @mail.uunet.ca:slee@hyper Thu Apr 21 15:41:54 1994 Subject: HyperChem Release 4 Now Available To: hyper!hyperchem@uunet.ca X-Mailer: ELM [version 2.3 PL9] Content-Length: 1205 X-Lines: 35 HyperChem Release 4 for Windows Now Available ============================================= Hypercube is pleased to announce that HyperChem Release 4 for Windows shipped on April 18, and is available from your HyperChem reseller. This release marks the return to Hypercube from Autodesk of the rights to sell and market HyperChem, and includes the following improvements: o HyperChem's interface now has a 3D look, and the tools have a convenient pop-up description. o The calculations have been speeded up, with some semi-empirical calculations a factor of two faster than Release 3. o HyperChem is now available in a Network version, suitable for running on local area networks. o The documentation has been updated to include all material new since Release 2 into the proper books. o Several bugs from Release 3 have been fixed. Suggested retail prices are, in US dollars: Purchase: $1995 ($995 Government and Educational Institutions) Upgrade from Release 3: $195 Upgrade from Release 2: $495 Network pricing is available on request. For more details concerning this release, please send e-mail to info@hyper.com. ----- End Included Message ----- From owner-software@net.bio.net Tue May 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!EU.net!ub4b!news.sri.ucl.ac.be!idefix.CS.kuleuven.ac.be!reks.uia.ac.be!derijkp From: derijkp@reks.uia.ac.be (Peter.DeRijk) Subject: DCSE 3.0 alignment editor for X-Windows Message-ID: <1994May4.164626.27367@reks.uia.ac.be> Keywords: alignment sequences structure Organization: U.I.A. X-Newsreader: Tin 1.1 PL5 Date: Wed, 4 May 1994 16:46:26 GMT Lines: 158 The multiple sequence alignment editor DCSE has been converted to X-windows, and is available for Silicon Graphics (IRIX). It uses the the great embedable language Tcl/Tk (Thanks, Dr. Ousterhout) for its interface. This way it is not only very easy to use, but also easily adaptable and extendable. Several interesting new features have been added (see attached readme file for more details). DCSE 3.0 is currently only available for SGI systems, but other systems will follow. We will be installing some PC's with Linux shortly, so this will most probably be the next. I also would like to do a port to Sun, but do not have acces to one at the moment. You can get DCSE v3.0 for X-Windows via anonymous ftp on uiam3.uia.ac.be (143.169.8.1). To get it, do the following: % ftp uiam3.uia.ac.be login as anonymous and give your email adress as a password. ftp> cd [.dcse] ftp> bin ftp> get TKDCSE-SGI-3_0.TAR_Z ftp> quit % mv TKDCSE-SGI-3_0.TAR_Z tkdcse=sgi-3.0.tar.Z % zcat tkdcse=sgi-3.0.tar.Z | tar xf - % cd tkdcse_home % install Then read the help, and follow further instructions. If you have problems with it, please contact me. Of course, if you think it is good, or have writen nice extensions to it, you may also contact me. Peter De Rijk derijkp@reks.uia.ac.be I have attached the readme file for DCSE 3.0 to this message. ================ readme =================== What is DCSE ------------ DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor. It can be used to edit protein, DNA or RNA alignments. The structure of the molecules can be incorporated in the alignment. It is written in C, and it uses dynamic memory for most things. This means you can almost edit any size of alignment with it. It offers lots of features such as color display of characters and structure, automatic alignment relative to sequences already aligned with others, sequence grouping, sequence or pattern searching, marker system, checking of incorporated RNA structure, on-line hypertext help, macros, and a lot more. This new version of DCSE has an easy to use, yet flexible and programmable X-windows interface provided by the Tcl/Tk language. A complete on-line hypertext help system is provided. Although DCSE v3.0 is compatible with the older version of DCSE, its implementation is completely different. The core of DCSE is implemented as an object which can be controlled by giving commands to it from the Tcl language, an easy to learn, yet flexible, interpreted language. The interface is written as a Tcl program. This way the program can be easily customized, and batch jobs are even possible. This approach has several advantages: - the user can adapt the interface of DCSE completely to his own liking. - It is easy to create macros or programs wich extend DCSE. - external programs can also be controlled in Tcl, and seamlessly integerated. - Tcl/Tk exists for a great variety of computers, so porting should be simplified. Convers is a complementary program to DCSE which does things like converting between different file-formats. The new version has been written a set of commandline programs, which are controlled by a Tcl/Tk interface. Legalities ---------- DCSE is Copyright Peter De Rijk, University of Antwerp (UIA), 1993 You may give this application to anyone, via any medium, so long as it is delivered with ALL the supplied files and UNALTERED, and it is not supplied on a disc you are charging for (except for media and postage costs). I maintain copyright on all the material supplied and reserve the right to amend these conditions in cases where I deem misuse. Disclaimer This application is supplied free to everyone 'as is', I do not give any guarantee that it is free of bugs, or supply any warranty about its suitability for use. No liability will be accepted for any damage to or loss of data as a result of using this application. However, if there are any problems with it and you notify me of them, I will probably do my best to rectify them. Citation A paper has been written about DCSE and this is submitted to and accepted by CABIOS. If you have used the program to obtain results in a paper you've written, please cite the following reference: Peter De Rijk and Rupert De Wachter DCSE v2.54, an interactive tool for sequence alignment and secondary structure research. Comput. Applic. Biosci. Reprints of articles in which DCSE is mentioned would be welcomed. I will do my best to reply as fast as I can to any problems, etc. . However, the development of DCSE is not my only task, which is why my response might not be always as fast as you would like. System ------ This program has been tested on an Indigo with an R4000 and on one with an R3000. It should work on other Silicon Graphics machines as well. Installing the package ---------------------- Uncompress and untar the distribution in a suitable directory. This will produce a directory called tkdcse_home. Go into that directory, and start the program install. Then follow directions. zcat tkdcse-sgi-3.0.tar.Z | tar xf - cd tkdcse_home ./install The install program will give you more info on what to do to install DCSE. The programs can be started by typing 'tkdcse' or 'tkconvers' in a shell window. Bugs ---- If you are having problems with the program contact me. I will do my best to get it fixed. Please report any bugs you have found. If possible, state your machine's hardware and software configurations. Sending me a full description of the circumstances in which the bug occurs, possibly with the data it happened on, will help me tracking down a bug. If you have any suggestions, you can also make them to me. How to contact me ----------------- Peter De Rijk University of Antwerp (UIA) Department of Biochemistry Universiteitsplein 1 B-2610 Antwerp tel.: 32-03-820.23.16 fax: 32-03-820.22.48 E-mail: derijkp@reks.uia.ac.be From owner-software@net.bio.net Tue May 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!overload.lbl.gov!dog.ee.lbl.gov!ihnp4.ucsd.edu!usc!howland.reston.ans.net!torn!news.ccs.queensu.ca!QUCDN.QueensU.CA!GERLACHJ From: GERLACHJ@QUCDN.QueensU.CA (Jim Gerlach) Subject: PPSP Package - Opinions? Message-ID: Lines: 14 Sender: news@knot.ccs.queensu.ca (Netnews janitor) Organization: Queen's University Date: Wed, 4 May 1994 14:37:11 GMT I received an ad for PPSP (Peptide-Protein Structure Prediction), an integrated, modular protein structure prediction package. The ad was limited on information but for $495 Canadian (~$375 US) it sounded interesting. Has anyone had any experience (good or bad) with this package? Any suggestions for alternatives? Thanx in advance for your help. Cheers, Jim ------- Jim Gerlach Cancer Research Laboratories gerlachj@qucdn (BITNET) Queen's University gerlachj@qucdn.queensu.ca (InterNet) Room A309, Botterell Hall tel (613) 545-6446 Kingston, Ontario fax (613) 545-6830 Canada K7L 3N6 From owner-software@net.bio.net Tue May 03 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!news.dfn.de!scsing.switch.ch!swidir.switch.ch!univ-lyon1.fr!news From: duret@evoserv.univ-lyon1.fr (Laurent Duret) Newsgroups: bionet.software Subject: Re: GeneWorks vs. DNAStar Date: 4 May 1994 06:18:23 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 35 Distribution: world Message-ID: <2q7enf$7f6@cismsun.univ-lyon1.fr> References: <1994May3.181321.1@samba.cnb.uam.es> Reply-To: duret@evoserv.univ-lyon1.fr NNTP-Posting-Host: evoserv.univ-lyon1.fr In article 1@samba.cnb.uam.es, lpezzi@samba.cnb.uam.es writes: > We are considering the purchase of GeneWorks of DNAStar for our institution. > > Any comments on the relative merits of both programs ? > > Thanks in advance > > Luis Pezzi > Centro Nacional de Biotecnologia > Madrid. Spain > Hola! You may have a look at the article by H. Mangalan in TIBS (18) may 1993 pp.187-188 who compared various sequence analysis programs among which Geneworks and DNAstar. Hasta luego, Laurent Duret ================================================================ Laboratoire de Biometrie, Genetique et Biologie des Populations Bat 741 - URA CNRS 243 Universite Claude Bernard - Lyon I 43, Bd du 11 Novembre 1918 69622 Villeurbanne cedex FRANCE Tel: +33 72.44.81.42 Fax: +33 78.89.27.19 E-mail: duret@biomserv.univ-lyon1.fr ================================================================ From owner-software@net.bio.net Tue May 03 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!newsserver.jvnc.net!raffles.technet.sg!nuscc.nus.sg!mpengtw From: mpengtw@leonis.nus.sg (Ng Tuck Wah) Newsgroups: bionet.software Subject: Software For Reference Management Date: 4 May 1994 07:44:59 GMT Organization: National University of Singapore Lines: 7 Message-ID: <2q7jpr$nlk@nuscc.nus.sg> NNTP-Posting-Host: leonis.nus.sg X-Newsreader: TIN [version 1.2 PL0] Dear fellow researcher, If you have need for a PC-based software to handle your reference material and do not intend to spend too much on it, please e-mail to mpengtw@leonis.nus.sg From owner-software@net.bio.net Wed May 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!gdt!aber!gepasi.dbs.aber.ac.uk!prm From: prm@aber.ac.uk (Pedro Mendes) Subject: Re: PC Protein _Viewing_. Message-ID: Keywords: RasMol Lines: 25 Sender: news@aber.ac.uk (USENET news service) Nntp-Posting-Host: pcfchb.dbs.aber.ac.uk Organization: The University of Wales Aberystwyth X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] References: <9405041823.AA02232@merlin.ciens.ula.ve> Distribution: bionet Date: Thu, 5 May 1994 11:31:05 GMT >Rob Smith writes: > I am interested in acquiring protein viewing software for a PC. I use >an SGI Iris with Quanta and CHARMm at lab but would like to be able to view >certain results graphically from home. Ideally, I would like something >that would allow me to display color SVGA stick figures, rotate them, >and even display van der Waals radii (as dots, not solids). High >resolution and the ability to rotate are essential as is low cost >(<$200). Any assistance is greatly appreciated. Thanks. Rob: One of the best programs for this is RasMol, which fits your bill very well since it is FREE SOFTWARE. The author of RasMol is currently working with people in Glaxo (so this can tell you of the quality of the software). You can get RasMol by FTP from: ftp.dcs.ed.ac.uk:/pub/rasmol/raswin.exe It may not do everything that you want but I garantee you that it is worth a look (and I'm sure you'll end up using it even if you get a commercial one...) Pedro Mendes prm@aber.ac.uk From owner-software@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!bjd12 From: bjd12@cus.cam.ac.uk (Ben Davis) Newsgroups: bionet.general,bionet.molbio.embldatabank,bionet.molbio.proteins,bionet.software Subject: databases search - protein size Date: 5 May 1994 11:36:17 GMT Organization: U of Cambridge, England Lines: 18 Message-ID: <2qalnh$36h@lyra.csx.cam.ac.uk> NNTP-Posting-Host: grus.cus.cam.ac.uk X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.general:8904 bionet.molbio.embldatabank:318 bionet.molbio.proteins:1879 bionet.software:8099 Hi I'm trying to find a way of searching databases for proteins (ideally from E.Coli) with a mass in a given range (say between 10 and 18 kDa). Anyone got any suggestions ? Ben -- ______________________________________________________________________________ Ben Davis, MRC Protein Function and Design, Cambridge, UK ______________________________________________________________________________ "They can make me do it, but they can't make me do it with dignity." From owner-software@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!qmw!UNL.AC.UK!11KLIEMC From: 11kliemc@unl.ac.uk Newsgroups: bionet.software Subject: Karyotype Representation Date: 5 May 1994 09:35:21 GMT Organization: University of North London Lines: 7 Message-ID: <2qaekp$ies@beta.qmw.ac.uk> Reply-To: 11kliemc@unl.ac.uk NNTP-Posting-Host: clstr.unl.ac.uk I am looking at possible data structures for the representation of karyotypes which will facilitate the matching of abnormalities with uncertainty. Does anyone know of any papers in this area? Thanks, Carol Kliem From owner-software@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!ysics.physics.sunysb.edu!adam.cc.sunysb.edu!psinntp!psinntp!alsys1!knockout.aecom.yu.edu!ness From: ness@aecom.yu.edu (seth ness) Newsgroups: bionet.software Subject: reading Image Quant files Message-ID: <2795@alsys1.aecom.yu.edu> Date: 4 May 94 14:07:13 GMT Sender: news@alsys1.aecom.yu.edu Organization: aecom Lines: 9 Nntp-Posting-Host: knockout.aecom.yu.edu X-Newsreader: Nuntius Version 1.2 X-XXMessage-ID: X-XXDate: Wed, 4 May 1994 15:07:19 GMT hi, how can i read image quant (molecular dynamics) files in another program. i've managed to open the 8 bit files in photoshop. But when i try to open the original 16 bit files i get garbage? seth ness ness@aecom.yu.edu From owner-software@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!uunet!hp81.prod.aol.net!search01.news.aol.com!not-for-mail From: alussow@aol.com (ALussow) Newsgroups: bionet.software Subject: reference software Date: 5 May 1994 00:53:09 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 4 Sender: news@search01.news.aol.com Message-ID: <2q9u3l$2i6@search01.news.aol.com> NNTP-Posting-Host: search01.news.aol.com I'm an immunologist looking for a good cheap reference manager. Any help would be much appreciated. Alex From owner-software@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!agate!headwall.Stanford.EDU!stout.Stanford.EDU!cherry From: cherry@stout.Stanford.EDU (Mike Cherry) Newsgroups: bionet.software Subject: FOGS #2 -- Wednesday, May 18th at Genentech Date: 5 May 1994 04:41:37 GMT Organization: Stanford University Genetics Department Lines: 72 Distribution: ca Message-ID: <2q9te1$73l@nntp2.Stanford.EDU> NNTP-Posting-Host: stout.stanford.edu ANNOUNCEMENT: "FOGS - Forum On Genomics and Sequence analysis" WHY? To provide an informal, quarterly forum where computer scientists and biologists working on genomic sequence analysis software and databases in the San Francisco Bay Area can meet to discuss and exchange ideas. WHEN? Second meeting May 18, 1994 (Wednesday) 6:30PM to 9:00PM WHERE? Genentech, South San Francisco. WHO? Anyone who is working on sequence analysis software and/or database development. Hopefully there will be at least one person from each of the academic and commercial organizations (e.g., Genentech, Stanford, LBL, LLNL, UC, etc.). FOGS is envisioned to be a relatively small and focused group, however the meetings will be open to anyone. WHAT? 1. Pizza dinner provided by Genentech during a Poster session. Roughly from 6:30 - 8:00PM. 2. Two presentations. From 8:00 - 9:00PM. David Botstein, Stanford U "title to be announced" Dan Gusfield, UC Davis "Some New Directions in Sequence Analysis." At this time there have been 10 people that stated they will be presenting a poster. Anyone is welcome to present a poster, however please let me know so we can have sufficient poster boards available. If you plan to attend FOGS #2 please RSVP to cherry@genome.stanford.edu. This will allow us to have plenty of pizza and beverages available. DIRECTIONS TO GENENTECH. Genentech is off US 101 in South San Francisco, this is north of the San Francisco Airport. From the North: - Take the 101 Freeway South - Exit at Grand Ave/South San Francisco - At the bottom of the ramp, turn left onto Airport Blvd. - At stop light, turn left onto Grand Ave. and proceed under freeway to East Grand Ave. - At the fourth stop light, turn left onto Forbes Blvd. - Continue on Forbes Blvd for 1.3 miles until it terminates at Point San Bruno Blvd. - Turn left into parking lot. The meeting will be in Building 5, the Genentech conference center. The entrance is on Forbes Blvd. From the South: - Take the 101 Freeway North - Exit at Grand Ave/South San Francisco - At the bottom of the ramp, turn right onto East Grand Ave. - At the first stop light, turn right to continue on East Grand Ave. - Proceed to left lane and turn left onto Forbes Blvd. - Continue on Forbes Blvd for 1.3 miles until it terminates at Point San Bruno Blvd. - Turn left into parking lot. The meeting will be in Building 5, the Genentech conference center. The entrance is on Forbes Blvd. By May 9th images of a map will be available on the nascent FOGS home page. URL: http://genome-www.stanford.edu/fogs-home.html Scooter Morris (scooter@gene.com) Mike Cherry (cherry@genome.stanford.edu) -- J. Michael Cherry Internet: cherry@genome.stanford.edu Head, Computing Stanford DNA Sequence & Tech. Center Project Manager Saccharomyces Genome Database Stanford University School of Medicine Stanford, CA 94305-5120 From owner-software@net.bio.net Wed May 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!news.cs.indiana.edu!nstn.ns.ca!newsflash.concordia.ca!sifon!NewsWatcher!user From: kwan@medcor.mcgill.ca (Tony Kwan) Subject: Fonts for amino acids Message-ID: Followup-To: bionet.software Sender: news@sifon.cc.mcgill.ca Organization: Department of Biochemistry, McGill University Date: Thu, 5 May 1994 15:17:15 GMT Lines: 10 I'm looking for a font that will has each letter of the alphabet enclosed in a circle. I, and others, would like to be able to draw diagrams of a protein and show each amino acid as a little circle (which can be done with any drawing program) but with the one-letter code inside it. Thanks. -- Tony Kwan Department of Biochemistry, McGill University kwan@medcor.mcgill.ca From owner-software@net.bio.net Wed May 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!emory!nigel.msen.com!zib-berlin.de!news.dfn.de!gwdu03.gwdg.de!flylab.mpib-tuebingen.mpg.de!user From: geisler@genvax.mpib-tuebingen.mpg.de (Robert Geisler) Subject: Re: Tektronix graphics on Mac Message-ID: Followup-To: bionet.software Sender: news@gwdu03.gwdg.de (USENET News System) Nntp-Posting-Host: flylab.mpib-tuebingen.mpg.de Organization: MPI fuer Entwicklungsbiologie References: <2q57uu$l08@mserv1.dl.ac.uk> Distribution: bionet Date: Thu, 05 May 1994 13:46:09 +0200 Lines: 17 In article <2q57uu$l08@mserv1.dl.ac.uk>, plxigpg@vax.ccc.nottingham.ac.uk wrote: > Can anyone tell me how to increase the size of a Tektronix graphics window > on a Mac. I'm using it for GCG graphics - but a lot of them do not > fit onto the screen. If you are referring to NCSA Telnet, get version 2.6. It has resizable Tektronix windows. However - both the 4014 and 4105 modes still appear to have problems with GCG (V7.3) graphics. Extra characters appear across the plot in 4014 mode, and the background color changes when redrawing the window in 4105 mode. You might consider buying VersaTerm Pro, which works fine with GCG in both modes. Regards, Robert From owner-software@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!agate!usenet.ins.cwru.edu!nigel.msen.com!zib-berlin.de!uni-paderborn.de!urmel.informatik.rwth-aachen.de!news.dfn.de!scsing.switch.ch!swidir.switch.ch!univ-lyon1.fr!jussieu.fr!zaphod.crihan.fr!news.univ-rennes1.fr!q800-neuro.univ-poitiers.fr!jpp From: J.P. Poindessault Newsgroups: bionet.software Subject: Retina response simulation Date: 4 May 1994 14:06:25 GMT Organization: CNRS U1869 LBSC, 86022 Poitiers -FRANCE- Lines: 10 Distribution: world Message-ID: <2q8a51$2ef@news.univ-rennes1.fr> NNTP-Posting-Host: q800-neuro.univ-poitiers.fr X-Newsreader: Nuntius Version 1.2 X-XXMessage-ID: X-XXDate: Wed, 4 May 1994 15:59:56 GMT For educational purpose, running on PC (Windows ?), we are looking for: software that simulates (models) electrical responses of the different cells in the retina following photonic stimulation (ionic currents, membrane potentials etc...) Thanks. ---------------------------------------------------------------------- Laboratoire de NeuroPhysiologie | tel: (33) 49 45 37 35 - M. ROGER CNRS, URA 1869, Biomembranes | (33) 49 45 38 53 - F. GAILLARD 86022 Poitiers Cedex FRANCE | fax: (33) 49 45 40 14 ---------------------------------------------------------------------- From owner-software@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!agate!library.ucla.edu!psgrain!nntp.cs.ubc.ca!utcsri!utnut!torn!news.unb.ca!coranto.ucs.mun.ca!nstn.ns.ca!psinntp!psinntp!pioneer.uspto.gov!pioneer.uspto.gov!not-for-mail From: garris@uspto.gov (Malinda Garris) Newsgroups: bionet.software Subject: WANTED: Biology Resources Date: 4 May 1994 13:59:40 -0400 Organization: United States Patent and Trademark Office Lines: 29 Message-ID: <2q8nqc$ilg@pioneer.uspto.gov> NNTP-Posting-Host: pioneer.uspto.gov X-Newsreader: TIN [version 1.2 PL2] We are working with the Patent and Trademark Office to identify potential sources of biotechnology information particularly nucleic and amino acid sequence databases available for public access using both the Internet and other databases/networks. If you are aware of such a database I would appreciate it if you could answer a few brief questions: 1. Identify the database--name of database, primary/ secondary items, one line description. 2. What sources contribute to the database? 3. How often is the database updated? Are entries "date-stamped"? 4. Address for general inquiry. If you e-mail responses I would be happy to summarize data and post to the group. Thanks in advance, Malinda J. Garris Librarian Garcia Consulting, Inc. ****Standard disclaimers apply**** From owner-software@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.reston.ans.net!torn!nott!uotcsi2!usenet From: misrael@grdb.csi.uottawa.ca (Mark Israel) Newsgroups: bionet.software Subject: Re: Fonts for amino acids Date: 5 May 1994 17:14:49 GMT Organization: Dept. of Computer Science, University of Ottawa Lines: 14 Message-ID: <2qb9i9$qmq@csi0.csi.uottawa.ca> References: NNTP-Posting-Host: grdb.csi.uottawa.ca X-ORIGINAL-NEWSGROUPS: bionet.software In article , Tony Kwan wrote: > I'm looking for a font that will has each letter of the alphabet enclosed > in a circle. I, and others, would like to be able to draw diagrams of a > protein and show each amino acid as a little circle (which can be done with > any drawing program) but with the one-letter code inside it. Thanks. What type of computer are you running on? For the IRIS, there's the Smartie program by Michael Murphy. Contact Ron Meleshko (ron@odysseus.biochem.ualberta.ca) to obtain this. misrael@csi.uottawa.ca Mark Israel From owner-software@net.bio.net Wed May 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!headwall.Stanford.EDU!MED.Stanford.EDU!cmgm.stanford.edu!klingler From: klingler@cmgm.stanford.edu (Tod Klingler) Subject: Re: Rasmol Message-ID: Sender: news@medmail.stanford.edu Organization: Stanford University, California, USA References: <2qai1d$hkv@mserv1.dl.ac.uk> Distribution: bionet Date: Thu, 5 May 1994 21:29:40 GMT Lines: 87 Pedro writes: >Can anybody tell me which is the last version of Rasmol? From where can it be > obtained by FTP? and finally, how many atoms can it handle? Thanks. RasMol 2.3 Molecular Graphics Visualisation tool. Roger Sayle BioMolecular Structures Group Glaxo Research & Development Greenford, Middlesex, UK. February 1994 RasMol is an X Window System tool intended for the visualisation of proteins and nucleic acids. It reads Brookhaven Protein Databank (PDB) files and interactively renders them in a variety of formats on either an 8bit or 24/32bit colour display. The complete source code and user documentation for the UNIX/X11, IBM PC/MSWindows and the VMS/DecWindows versions may be obtained by anonymous ftp from ftp.dcs.ed.ac.uk [129.215.160.5] in the directory /pub/rasmol. All the source code is contained in the file RasMol2.tar.Z and the MS Windows source code and executable in the file raswin.zip. Both of these files include on-line help, hypertext documentation and the previous (dated) version of the PostScript user reference manual. Please remember to use "binary" mode when transferring files between UNIX and MSDOS systems. Check that the file size is the same before and after transfer. The MSWindows error "No Memory for Application" is symptomatic of transfering "raswin.exe" in ASCII mode (corrupting it). The program is intended for teaching and generating publication quality images. The program has both a menu system and a full featured command line interface. Different parts and representations of the molecule may be coloured or displayed in a number of formats independently. Currently supported formats include wireframe, ball and stick, backbone, space filling spheres and solid or strands ribbon models. The space filling spheres may even be shadowed. The molecule may be manipulated using the mouse, the scroll bars, the interactive command line or from a dials box (if one is attached). The resulting image may be saved at any point in PostScript, GIF, PPM, Sun rasterfile or Microsoft BMP formats. For more details see the RasMol user reference. On a SparcStation, it can shadow a 10,000 atom spacefilling protein in less than 10 seconds. The current version of the program has been tested on sun3, sun4, sun386i, SGI, DEC & E&S mips based machines, DEC Alpha (OSF/1 and OpenVMS), VAX VMS (under Dec Windows), IBM RS/6000, hp9000, sequent compiled under both gcc and (typically) the native compiler. The version for Microsoft Windows requires version 7 of the Microsoft Optimizing C Compiler or Visual C++ Compiler and the Microsoft Software Development Kit (SDK). The source code is public domain and freely distributable provided that the original author is suitably acknowledged. Any comments, suggestions or questions about the package may be directed to either "rasmol@dcs.ed.ac.uk" or "rasmol@ggr.co.uk". Thank you for acquiring a copy of the RasMol distribution. I hope you enjoy it! If you like the program and decide to use it, *Please* send me a short email message to that effect, together with any comments or suggestions for improving the program. If you appreciate the large amount of work that has gone into creating RasMol, a small donation of $40 US or #25 GBP to the address below would be welcome. Contact Address: Roger Sayle, Department of Computer Science University of Edinburgh The King's Buildings, Mayfield Road, Edinburgh EH9 3JZ SCOTLAND Tel: (+44) 081 966 3567 (+44) 031 650 5163 EMail: ros@dcs.ed.ac.uk >================ >Dr. Pedro Candau >Departamento de Bioquimica Vegetal y Biologia Molecular >Universidad de Sevilla >Apdo. 1095, E-41080 Sevilla, Spain >e-mail Candau@CICA.Es >Tel. 34-5-4557082 >Fax 34-5-4620154 >=============================================================================== From owner-software@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: Pedro Newsgroups: bionet.software Subject: Rasmol Date: 5 May 1994 11:33:17 +0100 Lines: 21 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2qai1d$hkv@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk ------------------------------ Start of body part 1 Hi, Can anybody tell me which is the last version of Rasmol? From where can it be obtained by FTP? and finally, how many atoms can it handle? Thanks. ------------------------------ Start of body part 2 ================ Dr. Pedro Candau Departamento de Bioquimica Vegetal y Biologia Molecular Universidad de Sevilla Apdo. 1095, E-41080 Sevilla, Spain e-mail Candau@CICA.Es Tel. 34-5-4557082 Fax 34-5-4620154 =============================================================================== ------------------------------ End of body part 2 From owner-software@net.bio.net Wed May 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!uunet!nih-csl!helix.nih.gov!dspete From: dspete@helix.nih.gov (David S. Peterson) Subject: Re: reading Image Quant files Message-ID: Lines: 16 Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: National Institutes of Health X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] References: <2795@alsys1.aecom.yu.edu> Date: Thu, 5 May 1994 21:32:03 GMT In article <2795@alsys1.aecom.yu.edu> ness@aecom.yu.edu (seth ness) writes: >hi, >how can i read image quant (molecular dynamics) files in another program. >i've managed to open the 8 bit files in photoshop. But when i try to open >the original >16 bit files i get garbage? >seth ness >ness@aecom.yu.edu The 16 bit files are in a proprietary format. I doubt you'll find any application that will open then. David Peterson From owner-software@net.bio.net Wed May 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!sunic!trane.uninett.no!nac.no!dhhalden.no!pc138.dhhalden.no!arvidb From: arvidb@dhhalden.no (ARVID BARSTAD) Subject: Carbon copy Message-ID: Lines: 6 Sender: news@dhhalden.no (Network News User) Nntp-Posting-Host: pc138 Organization: Ostfold College X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Date: Thu, 5 May 1994 21:16:31 GMT I need a hint on where i could get Carbon copy. (ftp, fsp site). Any similar program could also be interesting. thanks in advance. Arvidb From owner-software@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!ELWHA.EVERGREEN.EDU!ottj From: ottj@ELWHA.EVERGREEN.EDU (Janet Ott) Newsgroups: bionet.software Subject: physiology software Date: 5 May 1994 14:53:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: bionet Message-ID: NNTP-Posting-Host: net.bio.net We just got an NSF grant to allow us to buy nine physiology stations which will include computers, all accompaningy transducers and a physiograph. I'm interested in two things. Does anyone out there do physiology with computers and transducers and if so, do you use Macs or PCs? Which of those do you think is more user friendly? WHich is more powerful? In short, which do you recommend? Secondly, which software do you recommend? I see LabView as the "default" but am curious if it really is the best out there for basic physiological studies. I'd really appreciate any input. Thanks in advance. Janet Ott, Ph. D. Lab I The Evergreen State College Olympia, Wa. 98505 206-866-6000, x6019 ottj@elwha.evergreen.edu From owner-software@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.reston.ans.net!EU.net!uknet!comlab.ox.ac.uk!oxuniv!oxpath!springer Newsgroups: bionet.software Subject: kinetics simulation Message-ID: <1994May5.113258.1@molbiol.ox.ac.uk> From: springer@molbiol.ox.ac.uk Date: 5 May 94 11:32:58 GMT Organization: Oxford University Molecular Biology Data Centre Nntp-Posting-Host: oxpath Nntp-Posting-User: springer Lines: 15 Dear All, I am trying to build a mathematical model for receptor-ligand binding that involves conformational change(s) upon binding. Is there such a thing as a good mathematical package that will simulate numerical solutions of differential equations, like Michaelis-Menten and all the more complicated ones? Ideas would be very much appreciated. Sebastian Springer, Oxford springer@vax.ox.ac.uk springer@molbiol.ox.ac.uk From owner-software@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!NATURE.BERKELEY.EDU!bosborne From: bosborne@NATURE.BERKELEY.EDU (Brian Osborne) Newsgroups: bionet.software Subject: .ps output in GCG? Date: 5 May 1994 17:38:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199405060038.RAA24651@nature.Berkeley.EDU> NNTP-Posting-Host: net.bio.net To the Group, I'm asking this question for a friend, so please forgive me if the answer is obvious. We are using GCG remotely, and we would like to make .ps files of various plots, then bring them back down to our Mac and print them. Can this be done? If so, how? I will summarize to the group. Thank you for your attention to this matter, Brian Osborne bosborne@nature.berkeley.edu From owner-software@net.bio.net Thu May 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!EU.net!chsun!cgchb!christo1 From: christo1@fmi.ch (Christen Tobias) Subject: Re: kinetics simulation Message-ID: <1994May6.064801.14873@ciba-geigy.ch> Sender: news@ciba-geigy.ch Nntp-Posting-Host: fmiunix Organization: Friedrich Miescher Institut (FMI), Basle, Switzerland References: <1994May5.113258.1@molbiol.ox.ac.uk> Date: Fri, 6 May 1994 06:48:01 GMT Lines: 24 Michaelis Menten sounds like you will not gonna extend your problem-description to a PDE-system, therefore any math-package like Maple, Mathematica or (!) Matlab are able to help you on. However you might even think of very nice interfaces to build your ODE-sets graphically, here I would recommend a Matlab-Simulink^ or Stella(=IThink)^^ software alot more packages of this sort exist but I donīt remember their names... Programs like Maple , Mathematica, and Matlab you might even get in your neighbourly scientific-bookstore. Cheers Tobias ^ = Mathworks ^^ = High Perfromance Systems (Hanover, NH) _________________________________________________________________________ Tobias F. Christen c/o Ciba Ltd K-125.14.42 Ph 2.2423 4002 Basel (Switzerland) From owner-software@net.bio.net Thu May 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!edvz.sbg.ac.at!wst!floeckn From: floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) Subject: Re: DCSE 3.0 alignment editor for X-Windows Message-ID: Keywords: alignment sequences structure Lines: 16 Sender: floeckn@wst (Floeckner Hannes) Reply-To: floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) Organization: University of Salzburg / Austria References: <1994May4.164626.27367@reks.uia.ac.be> Date: Fri, 6 May 1994 09:53:48 GMT We just installed DCSE 3.0 and it looks good. The only thing missing are manuals and documentation in printable form, I don't mean UNIX manual pages which are included. Is there a full manual or documentation of DCSE 3.0 available? hannes =========================================================================== Floeckner Hannes e-mail: floeckn@wst.edvz.sbg.ac.at Inst.f. Chemie und Biochemie Universitaet Salzburg Jakob-Haringerstr. 1 A-5020 Salzburg AUSTRIA - EUROPE From owner-software@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!usc!elroy.jpl.nasa.gov!swrinde!ihnp4.ucsd.edu!ucsnews!ucssun1.sdsu.edu!hsb From: hsb@ucssun1.sdsu.edu (Hirdeypal S. Bhathal) Newsgroups: bionet.software Subject: ***DNA Strider 3.0??????**** Date: 6 May 1994 02:12:27 GMT Organization: San Diego State University Lines: 11 Message-ID: <2qc92b$qku@gondor.sdsu.edu> NNTP-Posting-Host: 130.191.1.100 Hi netter Where and how can I get DNA strider 3.0. Thanks. Hirdeypal hsb@ucssun1.sdsu.edu From owner-software@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: chealy@crc.ac.uk (Dr. C.P. Healy) Newsgroups: bionet.software Subject: re:Enrtrez Date: 6 May 1994 15:53:08 +0100 Lines: 39 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2qdlkk$b7@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk To: larry.won@bbs.puc.edu Subject: Re: humanegene2 text file Newsgroups: bionet.general In-Reply-To: <9403091410571144@bbs.puc.edu> Organization: MRC Human Genome Resource Centre Cc: Bcc: In article <9403091410571144@bbs.puc.edu> you write: > First of all, I have to wonder why such important projects like >studies of human genes should have shortage of funds. I do not >understand why the United States spends so much money on extraneous >things for example, giving millions of dollars of "aid" to other >countries who can never pay us back. Especially when many times the >"aid" we give is misused and abused in that country. If the U.S. >would mind its won business and quit emphasizing foreign policy so >much than there would be mooney so that important projects like >the Human Genome Project would be able to carry out its task. > But that aside, I would think that the Genome Project people should >keep working on finding the entire human genome though their timetable >goal may not be met. Just concentrating on disease gene finding would >seem the most worthwhile thing to do with the shortage of money but in >the long run knowing the human genome will prove to be more >advantageous. > Knowing the human genome would be useful in so many different ways >because after you know the genome than scientists can work on what >physical effects genes have and kind of link together every tiny aspect >of the human body with specific genes. Dr. Chris Healy, Department of Craniofacial Development, UMDS, Guy's Hospital, LONDON, U.K. SE1 9JT e-mail: Chris Healy Tel: 071- 955-5000 From owner-software@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: "Bill Kupiec" Newsgroups: bionet.software Subject: Re: .ps from GCG Date: 6 May 1994 15:37:05 +0100 Lines: 22 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2qdkmh$sl8@mserv1.dl.ac.uk> Original-To: plxigpg@vax.nott.ac.uk, "Bio Software" RE>>.ps from GCG Ian writes: > Where can I get the LaserWriter Font utility? Does it come with the printer? Yes, it should be on one of your LaserWriter disks. Or, you could probably ftp in from Apple. > Any ideas? Print your plot to a ps file from GCG, ftp it to your Mac, and print directly using the LaserWriter Font utility. Personally I would bypass Cricket Graph. -Bill *------------------------------------------------------------* Bill Kupiec Operations Manager Carnegie Institution of Washington kupiec@mail1.ciwemb.edu *------------------------------------------------------------* From owner-software@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!GLUE.UMD.EDU!briwig From: briwig@GLUE.UMD.EDU (Brian Michael Wiegmann) Newsgroups: bionet.software Subject: ABI data and STADEN Date: 6 May 1994 07:22:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199405061423.KAA02925@phelix.umd.edu> NNTP-Posting-Host: net.bio.net I am using the November 1992 release of Staden and am having difficulty getting data from our ABI 373 automated sequencer into xbap. Our copy of staden is running under xwindows on a SPARCstation. the program is not recognizing the files in the ABI format. It is treating them as if they are regular sequence files (the contig editor shows the machine code of the ABI files as if it were sequence. Anyone out there have experience with, or special knowledge of, using xbap with ABI 373 files (includes traces etc.)?? Please contact me if you can help. thanks Brian Wiegmann Department of Entomology and Center for Agricultural Biotechnology University of Maryland From owner-software@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!SHIVA.PSU.EDU!zauhar From: zauhar@SHIVA.PSU.EDU (Dr. Randy Zauhar) Newsgroups: bionet.software Subject: Re: .ps output in GCG? Date: 5 May 1994 21:07:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9405060342.AA12406@shiva.psu.edu> NNTP-Posting-Host: net.bio.net Brian, It should be pretty easy to get the GCG output on your Mac - 1) Issue the "postscript" command, and choose encapsulated or color encapsulated postscript file. 2) For the "TERMinal", just give a file name. Your graphic output will now go into the file - you just have to transfer to your Mac (ftp, e.g.), and then import into an application. Depending on the app you want to use, you may need to resEdit the file so that the application will be able to recognize it. Hope that helps, Randy ///////////////////////////////////////////////////////////////////////// \\ Randy J. Zauhar, PhD | E-mail: zauhar@shiva.psu.edu // \\ Center for Computational Biology | Phone: (814) 863-3650 // \\ Penn State University | 865-1098 (after 5)// ///////////////////////////////////////////////////////////////////////// From owner-software@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Bill Kupiec" Newsgroups: bionet.software Subject: Re: .ps output in GCG? Date: 6 May 1994 12:33:30 +0100 Lines: 21 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2qd9ua$i2a@mserv1.dl.ac.uk> Original-To: "Bio Software" RE>>.ps output in GCG? Brian, Randy writes: > (stuff deleted)...then import ps file into an application. Or you can simply download the ps file directly to your printer using the LaserWriter Font Utility (from Apple). We do this process here and it works fine. Regards, -Bill *------------------------------------------------------------* Bill Kupiec Operations Manager Carnegie Institution of Washington kupiec@mail1.ciwemb.edu *------------------------------------------------------------* From owner-software@net.bio.net Thu May 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!gdt!aber!gepasi.dbs.aber.ac.uk!prm From: prm@aber.ac.uk (Pedro Mendes) Subject: Re: kinetics simulation Message-ID: Keywords: GEPASI Lines: 26 Sender: news@aber.ac.uk (USENET news service) Nntp-Posting-Host: pcfchb.dbs.aber.ac.uk Organization: The University of Wales Aberystwyth X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] References: <1994May5.113258.1@molbiol.ox.ac.uk> Date: Fri, 6 May 1994 11:18:42 GMT springer@molbiol.ox.ac.uk writes: >Is there such a thing as a good mathematical package that will simulate >numerical solutions of differential equations, like Michaelis-Menten and all >the more complicated ones? If you want to use a PC with Windows, you can use my metabolic simulator GEPASI. This is a dedicated simulation program (unlike Mathematica et al.) that uses the language of enzyme kinetics and metabolic control analysis, builds the ODEs automatically from the kinetic functions or reaction mechanisms and solves them. The program can be linked with GNUPLOT for producing plots of the simulation results and these can also be read into spreadsheet programs for further manipulation. If you want to try GEPASI, download it from: bmsdarwin.brookes.ac.uk:/pub/software/ibmpc/gepasi/gep208c.zip This is free software and the source code is available from the same site. Hope this helps Pedro Mendes prm@aber.ac.uk PS- the newsgroup bionet.metabolic-reg also deals with the subject of kinetics simulations (and in general metabolic simulations). From owner-software@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!news.funet.fi!news.csc.fi!convex!harper From: harper@convex.csc.FI (Rob Harper) Newsgroups: bionet.software Subject: Best of WWW '94 Nomenees Date: 6 May 1994 09:08:50 GMT Organization: CSC - Tieteellinen laskenta Lines: 13 Message-ID: <2qd1f2$jub@pobox.csc.fi> NNTP-Posting-Host: convex.csc.fi Keywords: www Well the best of WWW '94 nominees is now ready for reading. GDB and EXPASY are to the forefront for the biology servers. Check out who is doing what at the following URL http://wings.buffalo.edu/contest/vote/nominee.html RGDS -=ROB=- -- R. Andrew Harper E-mail: harper@convex.csc.fi Center for Scientific Computing Molbio/software: harper@nic.funet.fi Tietotie 6, P.O. Box 405 Telephone: +358 0 457 2076 SF-02101 Espoo Finland Fax: +358 0 457 2302 From owner-software@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!fuchs From: fuchs@embl-heidelberg.de (Rainer Fuchs (EMBL Data Library)) Newsgroups: bionet.software Subject: Updated MSU email server specification file Message-ID: <1994May4.150332.171094@eros.embl-heidelberg.de> Date: 4 May 94 15:03:32 +0100 Organization: EMBL Data Library Lines: 1767 Included is an up-to-date version of the service specification file used by the MSU mail server utility program. It now lists 26 email servers; recent additions include Bioccelerator, BioSCAN, EMBL PROSITE, SBASE, ProDom, and GCRDb. MSU simplifies access to Internet email servers by providing a customizable menu interface. MSU is available for UNIX and VAX systems from {ftp,gopher,www}.embl-heidelberg.de. -- Rainer Fuchs EMBL Data Library Fuchs@EMBL-Heidelberg.DE ================================================================================ ############################################################ # MSU default service specification file # Rainer Fuchs, EMBL Data Library # Fuchs@EMBL-Heidelberg.DE ############################################################ ### # EMBL Blitz server # 3-Dec-1993 ### service-name: EMBL BLITZ server service-info: Ultra-fast sequence comparisons on massively parallel computer service-addr: blitz@embl-heidelberg.de -- help-address: blitz@embl-heidelberg.de help-body: help // service-prot-options: start-token: SEQ end-token: END maxseqlen: 10000 -- msu-object: obj-name: Enter search title obj-info: This string will be used as the Subject of the return mail obj-tag: TITLE obj-class: String maxlen: 60 -- msu-object: obj-name: Value of PAM matrix obj-info: The amino acid weight matrix used to score non-identical amino acid pairs. obj-tag: PAM obj-class: Int min: 1 max: 500 def: 120 -- msu-object: obj-name: Enter gap penalty obj-info: Score for gaps in alignment obj-tag: INDEL obj-class: Int min: 5 max: 30 -- msu-object: obj-name: Enter number of best alignments obj-info: Number of alignments to show obj-tag: ALIGN obj-class: Int min: 1 max: 100 def: 30 -- msu-object: obj-name: Enter number of scores obj-info: Number of scores to report obj-tag: NAMES obj-class: Int min: 1 max: 100 def: 30 // no nuc options ### # Weizmann BIOCCELERATOR # 4-Mar-1994 ### service-name: BIOCCELERATOR service-info: BIOCCELERATOR installed at Weizmann Institute of Science, Israel service-addr: bicserv@sgbcd.weizmann.ac.il -- help-address: bicserv@sgbcd.weizmann.ac.il help-body: help // service-nuc-options: start-token: .. end-token: end seq-format: ascii lowercase: no maxseqlen: 10000 -- msu-object: obj-name: Select SW search obj-tag: Bic_sw obj-mandatory: y obj-class: Fixed -- msu-object: obj-name: Show alignments obj-info: Include alignments in output obj-tag: align obj-class: Boolean def: y -- msu-object: obj-name: Label your sequence obj-info: Assign a (short) name to your sequence obj-tag: begin obj-class: String def: Untitled // service-prot-options: start-token: .. end-token: end seq-format: ascii lowercase: no maxseqlen: 10000 -- msu-object: obj-name: Select database obj-info: Subset of database to be searched obj-tag: Bic_sw obj-mandatory: y obj-class: Group elements: 2 def: 1 items: -Infile2=SWISS:\*, -Infile2=PIR:\* -- msu-object: obj-name: Show alignments obj-info: Include alignments in output obj-tag: align obj-class: Boolean def: y -- msu-object: obj-name: Label your sequence obj-info: Assign a (short) name to your sequence obj-tag: begin obj-class: String def: Untitled ### # FLASH # 5-Oct-1993 ### service-name: FLASH service-info: Ultra-fast seq. comparisons. Registr. req. at dflash@watson.ibm.com service-addr: dflash@watson.ibm.com service-subject: dflash -- help-address: dflash@watson.ibm.com help-subject: dflash help-body: send help -- reg-address: dflash@watson.ibm.com reg-subject: Registration reg-options: msu-object: obj-name: Your name obj-tag: Name: obj-mandatory: y obj-class: String msu-object: obj-name: Your affiliation obj-tag: Affiliation: obj-mandatory: y obj-class: String msu-object: obj-name: Your postal address obj-tag: Address: obj-mandatory: y obj-class: String msu-object: obj-name: Your email address obj-tag: Email: obj-mandatory: y obj-class: String msu-object: obj-name: Your phone number obj-tag: Phone: obj-mandatory: y obj-class: String // service-prot-options: start-token: BEGIN end-token: 1 seq-format: fasta minseqlen: 30 maxseqlen: 1000 -- msu-object: obj-name: Enter PAM scoring matrix or leave blank and select BLOSUM matrix on next question obj-info: A value between 10 and 500 in multiples of ten. Higher values are optimal for more distantly related sequences; lower values are better for more similar sequences. 120 or 250 are good default values. obj-tag: PAM obj-class: Int min: 10 max: 500 -- msu-object: obj-name: Enter BLOSUM scoring matrix or leave blank if you entered a value for PAM matrix obj-info: A value out of 30,35,40,45,50,55,60,62,65,70,75,80,85,90, or 100. Higher values are better for more closely related sequences; lower values are better for detecting distant sequence similarity. 62 is a good default. obj-tag: BLOSUM obj-class: Int min: 30 max: 100 -- msu-object: obj-name: Enter number of best alignments obj-info: Number of alignments to show obj-tag: ALIGNMENTS obj-class: Int min: 1 max: 10000 def: 10000 -- msu-object: obj-name: Enter minimum score to report (threshold) obj-info: Only scores higher than the threshold are reported obj-tag: THRESHOLD obj-class: Int min: 30 max: 100 def: 50 ### # BioSCAN # 4-May-1994 ### service-name: BioSCAN service-info: Fast seq. comparisons using special-purpose hardware. service-addr: bioscan@cs.unc.edu -- help-address: bioscan@cs.unc.edu help-body: help // service-nuc-options: start-token: BEGIN seq-format: fasta -- msu-object: obj-name: Program name obj-tag: PROGRAM bscan obj-mandatory: y obj-class: Fixed -- msu-object: obj-name: Select database obj-info: Subset of database to be searched obj-tag: DATALIB obj-mandatory: y obj-class: Group elements: 15 def: 1 items: gb,gbbct,gbest,gbinv,gbmam,gbpat,gbphg,gbpln,gbpri,gbrna, gbrod,gbsyn,gbuna,gbvrl,gbvrt -- msu-object: obj-name: Report format obj-info: Specifies the format in which results will be delivered obj-tag: REPORT obj-class: Group elements: 5 def: 1 items: Segment,Simple,Align,Compress,None -- msu-object: obj-name: Statistical expectation obj-info: Cutoff score for reporting hits is calculated from this value obj-tag: EXPECT obj-class: Float min: 0.0001 max: 1000 def: 200 -- msu-object: obj-name: Substitution scoring matrix obj-info: Weight matrix for non-identical residue matches obj-tag: MATRIX obj-class: Group elements: 2 def: 1 items: DPAM47I,BLOSUMN // service-prot-options: start-token: BEGIN seq-format: fasta -- msu-object: obj-name: Program name obj-tag: PROGRAM bscan obj-mandatory: y obj-class: Fixed -- msu-object: obj-name: Select database obj-info: Subset of database to be searched obj-tag: DATALIB obj-mandatory: y obj-class: Group elements: 2 def: 1 items: sw,pir -- msu-object: obj-name: Report format obj-info: Specifies the format in which results will be delivered obj-tag: REPORT obj-class: Group elements: 5 def: 1 items: Segment,Simple,Align,Compress,None -- msu-object: obj-name: Statistical expectation obj-info: Cutoff score for reporting hits is calculated from this value obj-tag: EXPECT obj-class: Float min: 0.0001 max: 1000 def: 200 -- msu-object: obj-name: Substitution scoring matrix obj-info: Weight matrix for non-identical residue matches obj-tag: MATRIX obj-class: Group elements: 21 def: 4 items: PAM5,PAM30,PAM70,PAM120,PAM160,PAM180,PAM250,BLOSUM30,BLOSUM35, BLOSUM40,BLOSUM45,BLOSUM50,BLOSUM55,BLOSUM62,BLOSUM70,BLOSUM75, BLOSUM80,BLOSUM85,BLOSUM90,BLOSUM95,BLOSUM100 -- msu-object: obj-name: Apply filter obj-info: Eliminates biologically uninteresting reports obj-tag: FILTER obj-class: Boolean def: y ### # NCBI BLAST # 7-Oct-1993 ### service-name: NCBI BLAST service-info: BLAST similarity searches at the National Libr. of Medicine service-addr: blast@ncbi.nlm.nih.gov -- help-address: blast@ncbi.nlm.nih.gov help-body: help // service-nuc-options: start-token: BEGIN seq-format: fasta -- msu-object: obj-name: Select program to use obj-info: blastn is nucleotide seq vs. nucleotide db, blastx is translated nucleotide seq vs. protein db obj-tag: PROGRAM obj-mandatory: y obj-class: Group elements: 2 def: 1 items: blastn,blastx -- msu-object: obj-name: Select database obj-info: Subset of database to be searched obj-tag: DATALIB obj-mandatory: y obj-class: Group elements: 18 def: 1 items: nr, genbank, gbupdate, embl, emblu, pdb, vector,kabatnuc, dbest, epd, swissprot,pir,spupdate,genpept,gpupdate,kabatpro, tfd,palu -- msu-object: obj-name: Show histogram obj-info: Displays histogram of scores obj-tag: HISTOGRAM obj-class: Group elements: 2 def: 1 items: yes,no -- msu-object: obj-name: Enter number of scores (descriptions) obj-info: Number of scores to report obj-tag: DESCRIPTIONS obj-class: Int min: 1 max: 1000 def: 100 -- msu-object: obj-name: Enter number of high-scoring segment pairs (alignments) obj-info: Number of high-scoring segment pairs to report obj-tag: ALIGNMENTS obj-class: Int min: 1 max: 1000 def: 50 -- msu-object: obj-name: Scoring matrix for BLASTX (LEAVE BLANK FOR BLASTN searches!) obj-tag: MATRIX obj-class: Group elements: 4 items: BLOSUM62,PAM40,PAM120,PAM250 -- msu-object: obj-name: Return email address obj-info: An alternative email address to which results should be sent obj-tag: PATH obj-class: String // service-prot-options: start-token: BEGIN seq-format: fasta -- msu-object: obj-name: Select program to use obj-info: blastp is protein seq vs. protein db, tblastn is protein seq vs. translated nucleotide db obj-tag: PROGRAM obj-mandatory: y obj-class: Group elements: 2 def: 1 items: blastp, tblastn -- msu-object: obj-name: Select database obj-info: Subset of database to be searched obj-tag: DATALIB obj-mandatory: y obj-class: Group elements: 18 def: 1 items: nr,swissprot,pir,spupdate,genpept,gpupdate,pdb,kabatpro, tfd,palu, genbank, gbupdate, embl, emblu, pdb, vector,kabatnuc, dbest, epd -- msu-object: obj-name: Show histogram obj-info: Displays histogram of scores obj-tag: HISTOGRAM obj-class: Group elements: 2 def: 1 items: yes,no -- msu-object: obj-name: Enter number of scores (descriptions) obj-info: Number of scores to report obj-tag: DESCRIPTIONS obj-class: Int min: 1 max: 1000 def: 100 -- msu-object: obj-name: Enter number of high-scoring segment pairs (alignments) obj-info: Number of high-scoring segment pairs to report obj-tag: ALIGNMENTS obj-class: Int min: 1 max: 1000 def: 50 -- msu-object: obj-name: Scoring matrix applied for sequence comparisons obj-tag: MATRIX obj-class: Group elements: 4 items: BLOSUM62,PAM40,PAM120,PAM250 -- msu-object: obj-name: Apply filter obj-info: Eliminates biologically uninteresting reports obj-tag: FILTER obj-class: Boolean def: y -- msu-object: obj-name: Return email address obj-info: An alternative email address to which results should be sent obj-tag: PATH obj-class: String #### # EMBL FASTA server # 4-Oct-1993 ### service-name: EMBL FASTA server service-info: Protein and nucleotide database searches using the FASTA algorithm service-addr: fasta@embl-heidelberg.de -- help-address: fasta@embl-heidelberg.de help-body: help // service-nuc-options: start-token: SEQ end-token: END maxseqlen: 32000 -- msu-object: obj-name: Select database obj-info: Subset of database to be searched obj-tag: LIB obj-class: Group elements: 20 def: 1 items: EMALL,EMNEW,EFUN,EINV,EMAM,EORG,EPHG,EPLN,EPRI,EPRO,EROD,ESYN,EUNA,EVRL, EVRT,GBNEW,GBALL,GBONLY, GENEMBL, GENEW -- msu-object: obj-name: Enter k-tupel value (word size) obj-info: Controls the sensitivity of search. The lower the case the more sensitive the search, but also the longer the execution time obj-tag: WORD obj-class: Int min: 3 max: 6 def: 6 -- msu-object: obj-name: Enter number of scores obj-info: Number of scores to report obj-tag: LIST obj-class: Int min: 1 max: 100 def: 50 -- msu-object: obj-name: Enter number of best alignments obj-info: Number of alignments to report obj-tag: ALIGN obj-class: Int min: 1 max: 30 def: 10 -- msu-object: obj-name: Search one strand only obj-info: Search one strand only. By default, both strands will be searched obj-tag: ONE obj-class: Boolean def: no -- msu-object: obj-name: Enter search title obj-info: This string will be used as the Subject of the return mail obj-tag: TITLE obj-class: String maxlen: 60 // service-prot-options: start-token: SEQ end-token: END maxseqlen: 32000 -- msu-object: obj-name: Select database obj-info: Subset of database to be searched obj-tag: LIB obj-class: Group elements: 8 def: 1 items: SWALL, SWNEW, SW, NBRF, PIRONLY, SWISSPIRALL, BROOKHAVEN, NRL -- msu-object: obj-name: Enter k-tupel value (word size) obj-info: Controls the sensitivity of search. The lower the case the more sensitive the search, but also the longer the execution time obj-tag: WORD obj-class: Int min: 1 max: 2 def: 2 -- msu-object: obj-name: Enter number of scores obj-info: Number of scores to report obj-tag: LIST obj-class: Int min: 1 max: 100 def: 50 -- msu-object: obj-name: Enter number of best alignments obj-info: Number of alignments to report obj-tag: ALIGN obj-class: Int min: 1 max: 30 def: 10 -- msu-object: obj-name: Enter search title obj-info: This string will be used as the Subject of the return mail obj-tag: TITLE obj-class: String maxlen: 60 #### # PIR FASTA server # 6-Oct-1993 ### service-name: NBRF/PIR FASTA server service-info: Protein database searches using the FASTA algorithm service-addr: fileserv@nbrf.georgetown.edu -- help-address: fileserv@nbrf.georgetown.edu help-body: help search // service-nuc-options: seq-format: pir end-token: END SEARCH -- msu-object: obj-name: Enter k-tupel value (word size) obj-info: Controls the sensitivity of search. The lower the case the more sensitive the search, but also the longer the execution time obj-tag: SEARCH KTUP= obj-class: Int min: 3 max: 6 def: 6 // service-prot-options: seq-format: pir end-token: END SEARCH -- msu-object: obj-name: Enter k-tupel value (word size) obj-info: Controls the sensitivity of search. The lower the case the more sensitive the search, but also the longer the execution time obj-tag: SEARCH KTUP= obj-class: Int min: 1 max: 2 def: 2 ### # EMBL QuickSearch # 4-Oct-1993 ### service-name: EMBL QuickSearch server service-info: Rapid comparisons of nucleotide sequences, looking for close matches. service-addr: quick@EMBL-Heidelberg.DE -- help-address: quick@EMBL-Heidelberg.DE help-body: help // service-nuc-options: start-token: SEQ end-token: END maxseqlen: 100000 -- msu-object: obj-name: Select sequence library obj-info: Subset of database to be searched obj-tag: LIB obj-class: Group elements: 2 def: 1 items: ALL,GENEW -- msu-object: obj-name: Enter window size obj-info: Decreasing the window size will increase the sensitivity of the comparison. Leave blank if you don't know what you are doing obj-tag: WINDOW obj-class: Int min: 1 max: 50 -- msu-object: obj-name: Enter stringency obj-info: Decreasing the window size will increase the sensitivity of the comparison. Leave blank if you don't know what you are doing obj-tag: STRINGENCY obj-class: Int min: 1 max: 50 -- msu-object: obj-name: Set Perfect flag obj-info: Only perfect matches will be found obj-tag: PERFECT obj-class: Boolean def: no -- msu-object: obj-name: Enter minimum percentage of matches obj-info: Only hits with overlaps of more than n% identity will be presented obj-tag: MATCH obj-class: Int min: 0 max: 100 def: 90 -- msu-object: obj-name: Use local homology alignment obj-info: If set to yes, a local homology algorithm will be used. By default, a Needleman-Wunsch alignment is created obj-tag: BEST obj-class: Boolean def: no -- msu-object: obj-name: Search one strand only obj-info: Search one strand only. By default, both strands will be searched obj-tag: ONE obj-class: Boolean def: no -- msu-object: obj-name: Enter title of sequence obj-info: Short description of the sequence. Will be used as the Subject line of the reply obj-tag: TITLE obj-class: String maxlen: 70 // no prot options ### # CBRG (ETH Zuerich) ### service-name: CBRG (ETH Zuerich) service-info: Exhaustive search of SWISS-PROT protein sequence database service-addr: cbrg@inf.ethz.ch -- help-address: cbrg@inf.ethz.ch help-subject: help help-body: help // service-nuc-options: start-token: NuclPepSearch lowercase: no -- service-prot-options: start-token: PepPepSearch lowercase: no ### # BLOCKS server # 4-Oct-1993 ### service-name: BLOCKS server service-info: Comparison of protein or DNA sequences against database of protein blocks service-addr: blocks@howard.fhcrc.org -- help-address: blocks@howard.fhcrc.org help-body: help // service-prot-options: seq-format: fasta // service-nuc-options: seq-format: fasta ### # Mail-PROSITE # 26-Apr-1994 ### service-name: EMBL PROSITE server service-info: Pattern searches using PROSITE database service-addr: prosite@embl-heidelberg.de -- help-address: prosite@embl-heidelberg.de help-body: help // service-prot-options: start-token: SEQ seq-format: ascii end-token: END -- msu-object: obj-name: Enter search title obj-info: This string will be used as the Subject of the return mail obj-tag: TITLE obj-class: String maxlen: 60 --- msu-object: obj-name: Include abundant patterns in search obj-info: Include abundant patterns. By default, they are excluded. obj-tag: FULL obj-class: Boolean def: no // no nuc options ### # MotifFinder ### service-name: MotifFinder service-info: Motif finding tool at genome.ad.jp service-addr: motif@genome.ad.jp -- help-address: motif@genome.ad.jp help-body: help // service-prot-options: seq-format: fasta -- msu-object: obj-name: Select motif library obj-info: The motif library to be searched obj-tag: DATALIB obj-class: group elements: 2 def: 1 items: Prosite,MotifDic // no nuc options ### # ProteinPredict # 4-Oct-1993 ### service-name: ProteinPredict service-info: Neural network secondary protein structure prediction service-addr: PredictProtein@embl-heidelberg.de -- help-address: PredictProtein@embl-heidelberg.de help-subject: help // service-prot-options: -- msu-object: obj-name: Your name obj-info: Enter your full name here obj-tag: name: obj-mandatory: y obj-class: string maxlen: 60 -- msu-object: obj-name: Your address (part1) obj-info: Enter your postal address here obj-tag: address1: obj-mandatory: y obj-class: string maxlen: 60 -- msu-object: obj-name: Your address (part2) obj-info: Enter your postal address here obj-tag: address2: obj-mandatory: n obj-class: string maxlen: 60 -- msu-object: obj-name: Your email address obj-info: Enter your email address here obj-tag: email: obj-mandatory: y obj-class: string maxlen: 60 -- msu-object: obj-name: Enter sequence description obj-info: A brief description of the sequence obj-tag: # obj-mandatory: y obj-class: string maxlen: 78 // no nuc options ### # nnpredict # 4-Oct-1993 ### service-name: nnpredict service-info: Neural network secondary protein structure prediction service-addr: nnpredict@celeste.ucsf.edu -- help-address: nnpredict@celeste.ucsf.edu help-subject: help help-body: help // service-prot-options: lowercase: n seq-format: fasta -- msu-object: obj-name: Select prediction options obj-info: nnpredict uses the secondary structure class for prediction: (n) use no tertiary structure class for prediction (the default) (a) use all-alpha tertiary structure class for prediction (b) use all-beta tertiary structure class for prediction (a/b) use alpha/beta tertiary structure class for prediction obj-tag: option: obj-class: Group elements: 4 def: 1 items: n,a,b,a/b // no nuc options ### # NetGene # 4-Oct-1993 ### service-name: NetGene service-info: Neural network prediction of splice sites in vertebrates service-addr: netgene@virus.fki.dth.dk -- help-address: netgene@virus.fki.dth.dk help-subject: help help-body: help // service-nuc-options: seq-format: fasta minseqlen: 451 maxseqlen: 100000 // no prot options ### # Grail # 4-Oct-1993 ### service-name: Grail service-info: Gene finding service. Registration required at grail@ornl.gov service-addr: grail@ornl.gov -- help-address: grail@ornl.gov help-body: help -- reg-address: grail@ornl.gov reg-subject: Registration reg-options: msu-object: obj-name: Your name obj-tag: Name: obj-mandatory: y obj-class: String msu-object: obj-name: Your affiliation obj-tag: Affiliation: obj-mandatory: y obj-class: String msu-object: obj-name: Your postal address obj-tag: Address: obj-mandatory: y obj-class: String msu-object: obj-name: Your email address obj-tag: Email: obj-mandatory: y obj-class: String msu-object: obj-name: Your phone number obj-tag: Phone: obj-mandatory: y obj-class: String // service-nuc-options: seq-format: fasta minseqlen: 100 maxseqlen: 100000 -- msu-object: obj-name: Your GRAIL user ID obj-info: Enter the user id you received when registering with GRAIL obj-tag: Sequences 1 obj-class: String // no prot options ### # GeneID # 4-Oct-1993 ### service-name: GeneID (less than 20kb) service-info: Pediction of exons and gene structure. service-addr: geneid@darwin.bu.edu -- help-address: geneid@darwin.bu.edu help-body: help // service-nuc-options: start-token: Genomic Sequences seq-format: fasta minseqlen: 100 maxseqlen: 20000 -- msu-object: obj-name: Suppress automatic comparison of best model with protein database obj-info: The top-ranking model will NOT be submitted to NCBI's BLAST server obj-tag: Genomic Sequence -noblast obj-class: Boolean def: no // no prot options ### # GenMark # 4-Oct-1993 ### service-name: GenMark service-info: Gene finding service. Registration required at genmark@ford.gatech.edu service-addr: genmark@ford.gatech.edu service-subject: genmark -- help-address: genmark@ford.gatech.edu help-subject: instructions -- reg-address: genmark@ford.gatech.edu reg-subject: Registration reg-options: msu-object: obj-name: Your name obj-tag: Name: obj-mandatory: y obj-class: String msu-object: obj-name: Your affiliation obj-tag: Affiliation: obj-mandatory: y obj-class: String msu-object: obj-name: Your postal address obj-tag: Address: obj-mandatory: y obj-class: String msu-object: obj-name: Your email address obj-tag: Email: obj-mandatory: y obj-class: String msu-object: obj-name: Your phone number obj-tag: Phone: obj-mandatory: y obj-class: String // service-nuc-options: start-token: data -- msu-object: obj-name: Select species matrix obj-info: Matrix used to analyze submitted sequence obj-tag: SPECIES obj-class: Group elements: 4 def: 1 items: ecoli, hiexpress,ecophage, human -- msu-object: obj-name: Enter title of analysis obj-info: Short description of the sequence. Will be used as identifier in the reply. obj-tag: TITLE obj-class: String -- msu-object: obj-name: Select graphical output (PostScript file) obj-info: Will deliver results in the form of a Postscript File obj-tag: PSGRAPH obj-class: Boolean def: n -- msu-object: obj-name: Return CDS predictions with regions obj-info: GenMark replies with a list of regions containing possible coding regions from stop codon to stop codon obj-tag: PROTEIN region obj-class: Boolean def: n -- msu-object: obj-name: Return CDS predictions with ORFs obj-info: GenMark replies with a list of open reading frames (splice site to splice site) obj-tag: PROTEIN orf obj-class: Boolean def: n -- msu-object: obj-name: Send predicted ORFs automatically to BLAST server obj-info: ORFs in which coding regions are predicted are automatically submitted to NCBI's BLAST server for homology searches obj-tag: PROTEIN send obj-class: Boolean def: n -- msu-object: obj-name: Send nucleotide sequences of predicted ORFs automatically to BLAST server obj-info: Nucleotide sequences of ORFs in which coding regions are predicted are automatically submitted to NCBI's BLAST server for homology searches obj-tag: NUCSEQ send obj-class: Boolean def: n -- msu-object: obj-name: Select ORF list display format obj-info: orf gives detailed assessment of regions between splice-sites that are predicted to contain coding regions; region cites regions from stop codon to stop codon in which a coding region was predicted; off tells GenMark not to reply with an ORF list obj-tag: ORFLIST obj-class: Group elements: 3 def: 1 items: orf, region, off -- msu-object: obj-name: Enter alternative email address obj-info: Fill in if GenMark should use alternative email address obj-tag: ADDRESS obj-class: String -- msu-object: obj-name: Enter user name obj-info: You may fill in your name here for identification purposes obj-tag: NAME obj-class: String -- msu-object: obj-name: Enter Markov chain order obj-info: Specifies the order of the Markov chain used to analyze the sequence. Should be unnecessary to specify obj-tag: ORDER obj-class: Int /* Don't know whether these values have any resemblance to reality */ min: 1 max: 10 -- msu-object: obj-name: Enter window size obj-info: Length of the analysis window that the GenMark algorithm uses. Smaller values will produce a higher rate of false signals, but may show smaller coding regions. Larger values will clarify the signal of larger regions but yield lower sensitivity. Should be unnecessary to modify obj-tag: WINDOW obj-class: Int min: 1 max: 100000 def: 96 -- msu-object: obj-name: Enter window step size obj-info: Step size that the GenMark algorithm uses to advance the window. Smaller values increase the resolution of a graph and increases the output size. Should be unnecessary to modify obj-tag: STEP obj-class: Int min: 1 max: 100000 def: 12 -- msu-object: obj-name: Enter prediction threshold obj-info: This threshold will be used to judge whether a region should be predicted as coding obj-tag: THRESHOLD obj-class: Float min: 0 max: 1 def: 0.6 // no prot options ### # Pythia # 4-Oct-1993 ### service-name: PYTHIA (Rpts) service-info: Identification of occurrences of repetitive DNA elements service-addr: pythia@anl.gov service-subject: Rpts -- help-address: pythia@anl.gov help-subject: help // service-nuc-options: seq-format: ig maxseqlen: 10000 lowercase: no // service-name: PYTHIA (Alu) service-info: Identification of subfamily membership of Alu sequences service-addr: pythia@anl.gov service-subject: Alu -- help-address: pythia@anl.gov help-subject: help // service-nuc-options: seq-format: ig maxseqlen: 10000 lowercase: no ### # GenomeNet BLAST # 5-Oct-1993 ### service-name: GenomeNet BLAST service-info: BLAST similarity searches on the Japanese GenomeNet server service-addr: blast@genome.ad.jp -- help-address: blast@genome.ad.jp help-body: help // service-nuc-options: start-token: BEGIN seq-format: fasta -- msu-object: obj-name: Select program to use obj-info: blastn is nucleotide seq vs. nucleotide db, blastx is translated nucleotide seq vs. protein db obj-tag: PROGRAM obj-mandatory: y obj-class: Group elements: 2 def: 1 items: blastn,blastx -- msu-object: obj-name: Select database obj-info: Subset of database to be searched obj-tag: DATALIB obj-mandatory: y obj-class: Group elements: 7 def: 1 items: nr-nt, genbank, embl,nr-aa, swissprot, pir,prf -- msu-object: obj-name: Enter number of scores obj-info: Number of scores to report obj-tag: V= obj-class: Int min: 1 max: 1000 def: 500 -- msu-object: obj-name: Enter number of high-scoring segment pairs obj-info: Number of high-scoring segment pairs to report obj-tag: B= obj-class: Int min: 1 max: 1000 def: 250 -- msu-object: obj-name: Enter score for matches obj-info: The score to assign to a single-letter match obj-tag: M= obj-class: Int min: 1 max: 1000 def: 5 -- msu-object: obj-name: Enter score for mismatches obj-info: The score to assign to a single-letter mismatch obj-tag: N= obj-class: Int min: -1000 max: -1 def: -4 // service-prot-options: start-token: BEGIN seq-format: fasta -- msu-object: obj-name: Select program to use obj-info: blastp is protein seq vs. protein, tblastn is protein seq vs. translated nucleotide db obj-tag: PROGRAM obj-class: Group elements: 2 def: 1 items: blastp,tblastn -- msu-object: obj-name: Select database obj-info: Subset of database to be searched obj-tag: DATALIB obj-mandatory: y obj-class: Group elements: 7 def: 1 items: nr-aa, swissprot,pir,prf,pdbstr, nr-nt, genbank,embl -- msu-object: obj-name: Enter number of scores obj-info: Maximum number of scores to report obj-tag: V= obj-class: Int min: 1 max: 1000 def: 500 -- msu-object: obj-name: Enter number of high-scoring segment pairs obj-info: Maximum number of high-scoring segment pairs to report obj-tag: B= obj-class: Int min: 1 max: 1000 def: 250 ### # GenomeNet FASTA # 5-Oct-1993 ### service-name: GenomeNet FASTA service-info: FASTA similarity searches on the Japanese GenomeNet server service-addr: fasta@genome.ad.jp -- help-address: fasta@genome.ad.jp help-body: help // service-nuc-options: start-token: BEGIN seq-format: fasta -- msu-object: obj-name: Select database obj-info: Subset of database to be searched obj-tag: DATALIB obj-mandatory: y obj-class: Group elements: 30 def: 1 items: nr-nt, genbank,genbank-upd, genbank/primate,genbank/rodent, genbank/other_mammalian,genbank/other_vertebrate,genbank/invertebrate, genbank/plant,genbank/bacterial,genbank/structural_rna, genbank/viral,genbank/phage,genbank/synthetic,genbank/unannotated, genbank/est,genbank/patent, embl,embl/bacteriophage,embl/fungi, embl/invertebrate,embl/organelle,embl/other_mammalian, embl/other_vertebrate,embl/plant,embl/primate,embl/prokaryote, embl/rodent,embl/synthetic,embl/unannotated,embl/viral -- msu-object: obj-name: Enter k-tupel value (word size) obj-info: Controls the sensitivity of search. The lower the case the more sensitive the search, but also the longer the execution time obj-tag: KTUP obj-class: Int min: 3 max: 6 def: 6 -- msu-object: obj-name: Enter number of scores obj-info: Number of scores to report obj-tag: -b obj-class: Int min: 1 max: 100 def: 50 -- msu-object: obj-name: Enter number of best alignments obj-info: Number of alignments to report obj-tag: -d obj-class: Int min: 1 max: 100 def: 10 // service-prot-options: start-token: BEGIN seq-format: fasta -- msu-object: obj-name: Select program to use obj-info: FASTA is protein seq vs. protein db, TFASTA is protein seq vs. translated nucleotide db obj-tag: PROGRAM obj-class: Group elements: 2 def: 1 items: fasta,tfasta -- msu-object: obj-name: Select database obj-info: Subset of database to be searched obj-tag: DATALIB obj-mandatory: y obj-class: Group elements: 35 def: 1 items: nr-aa, swissprot,pir,prf,pdbstr, nr-nt, genbank,genbank-upd, genbank/primate,genbank/rodent, genbank/other_mammalian,genbank/other_vertebrate,genbank/invertebrate, genbank/plant,genbank/bacterial,genbank/structural_rna, genbank/viral,genbank/phage,genbank/synthetic,genbank/unannotated, genbank/est,genbank/patent, embl,embl/bacteriophage,embl/fungi, embl/invertebrate,embl/organelle,embl/other_mammalian, embl/other_vertebrate,embl/plant,embl/primate,embl/prokaryote, embl/rodent,embl/synthetic,embl/unannotated,embl/viral -- msu-object: obj-name: Enter k-tupel value (word size) obj-info: Controls the sensitivity of search. The lower the case the more sensitive the search, but also the longer the execution time obj-tag: KTUP obj-class: Int min: 1 max: 2 def: 2 -- msu-object: obj-name: Enter number of scores obj-info: Number of scores to report obj-tag: -b obj-class: Int min: 1 max: 100 def: 50 -- msu-object: obj-name: Enter number of best alignments obj-info: Number of alignments to report obj-tag: -d obj-class: Int min: 1 max: 100 def: 10 ### # GenQuest (Q) # 1-Nov-1993 ### service-name: GenQuest (Q) service-info: Database searches service-addr: q@ornl.gov -- help-address: q@ornl.gov help-body: help // service-nuc-options: start-token: SEQ end-token: END seq-format: ascii -- msu-object: obj-name: Sequence type obj-tag: TYPE DNA obj-mandatory: y obj-class: Fixed -- msu-object: obj-name: Select database obj-info: Database to be searched obj-tag: TARGET obj-class: Group elements: 2 def: 1 items: GSDB, Repetitive -- msu-object: obj-name: Select search method obj-info: Search method to be used (SW = Smith-Waterman) obj-tag: METHOD obj-class: Group elements: 4 def: 1 items: SW, FASTA, BLAST, FLASH -- msu-object: obj-name: Apply filter for repetitive sequences obj-info: Removes repetitive elements from query sequence obj-tag: FILTER obj-class: Boolean def: y -- msu-object: obj-name: Enter comment obj-info: To tag your sequence with some identifier obj-tag: COMMENT obj-class: String -- msu-object: obj-name: Enter number of scores (only for SW searches) obj-info: Number of scores to report obj-tag: SCORE obj-class: Int min: 1 max: 1000 def: 10 -- msu-object: obj-name: Enter number of alignments (only for SW searches) obj-info: Number of alignments to report obj-tag: ALIGN obj-class: Int min: 1 max: 1000 def: 10 // service-prot-options: start-token: SEQ end-token: END seq-format: ascii -- msu-object: obj-name: Sequence type obj-tag: TYPE PROTEIN obj-mandatory: y obj-class: Fixed -- msu-object: obj-name: Select database obj-info: Database to be searched obj-tag: TARGET obj-class: Group elements: 3 def: 1 items: SWISSPROT, PDB, PROSITE -- msu-object: obj-name: Select search method obj-info: Search method to be used (SW = Smith-Waterman) obj-tag: METHOD obj-class: Group elements: 4 def: 1 items: SW, FASTA, BLAST, FLASH -- msu-object: obj-name: Scoring matrix obj-info: Scoring matrix applied for sequence comparisons obj-tag: MATRIX obj-class: Group elements: 5 def: 1 items: BLOSUM60, BLOSUM80, PAM40, PAM120, PAM250 -- msu-object: obj-name: Enter comment obj-info: To tag your sequence with some identifier obj-tag: COMMENT obj-class: String -- msu-object: obj-name: Enter number of scores (only for SW searches) obj-info: Number of scores to report obj-tag: SCORE obj-class: Int min: 1 max: 1000 def: 10 -- msu-object: obj-name: Enter number of alignments (only for SW searches) obj-info: Number of alignments to report obj-tag: ALIGN obj-class: Int min: 1 max: 1000 def: 10 ### # SBASE Mail server # 10-Dec-1993 ### service-name: SBASE service-info: Protein domain detection service-addr: sbase@icgeb.trieste.it -- help-address: sbase@icgeb.trieste.it help-body: help // service-prot-options: start-token: BEGIN seq-format: FASTA -- msu-object: obj-name: Include annotation obj-info: Include complete annotation of domains in output obj-tag: ANNOTATIONS obj-class: Group elements: 2 def: 1 items: YES, NO -- msu-object: obj-name: Scoring matrix obj-info: Scoring matrix applied for sequence comparisons obj-tag: MATRIX obj-class: Group elements: 5 def: 1 items: PAM120, PAM250, PAM40, BLOSUM60, BLOSUM80 -- msu-object: obj-name: Cutoff score obj-info: Cutoff score for displaying homologies obj-tag: SCORE PARAMETER obj-class: Int min: 30 max: 100 def: 35 ### # ProDom # 14-Mar-1994 ### service-name: ProDom service-info: ProDom domain searches service-addr: prodom@toulouse.inra.fr -- help-address: prodom@toulouse.inra.fr help-body: help // service-nuc-options: start-token: BEGIN end-token: END seq-format: fasta -- msu-object: obj-name: Search type obj-tag: PROGRAM blastx obj-mandatory: y obj-class: Fixed // service-prot-options: start-token: BEGIN end-token: END seq-format: fasta -- msu-object: obj-name: Search type obj-tag: PROGRAM blastp obj-mandatory: y obj-class: Fixed ### # GCRDb # 26-Apr-1994 ### service-name: GCRDb (G-protein coupled receptors) service-info: FASTA searches of G-protein-coupled receptor database service-addr: gcrdb@receptor.mgh.harvard.edu -- help-address: gcrdb@receptor.mgh.harvard.edu help-body: help // service-prot-options: seq-format: fasta // From owner-software@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!FARBER.HARVARD.EDU!morrison From: morrison@FARBER.HARVARD.EDU (Paul Morrison) Newsgroups: bionet.software Subject: Re: Request info on AB373 sequencer STRETCH upgrade Date: 6 May 1994 14:21:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 38 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9405062122.AA17325@farber.harvard.edu> NNTP-Posting-Host: net.bio.net briwig@GLUE.UMD.EDU (Brian Michael Wiegmann) writes: >Has anyone out there used, or know people that have used, the new Applied >Biosystems stretch upgrade for the AB373 DNA sequencer. > >Does it work as well as they claim ? I have had part one of the two part process of the "stretch" upgrade installed for a month. 20 gels X ~ 34 lanes. Conlusions: The $15,000.00 when I first heard the number seemed to be a little steep but I am completely satisfied with the results. Using Dye terminator, ds DNA and Taq, the 350-450 runs to the first N (after editing) are now going out to 500-600. Forget these numbers because everyone does different amounts of editing. Bottom line, we are getting about 20% more base calls. When considering walking in and closure on a gene, a 20% increase in length does wonders. Now for a little good news/bad news. Part one drops the optics bench 10cm so the well to read of the laser is that much longer. By changing the % gel and the watts the analysis package is faked out and thinks everything is normal,(the present algorithm fits). Part two of the upgrade gives you longer glass so the well to read increases by another 10 cm. Unfortunately the software can't be faked out _that_ much. PE/ABD is working feverishly on Analysis 2.0 that will be the answer to are dreams. (yeah right). No really. Somehow with a combo of dye primers and or Sequanase or Taq you can fake out the software. PE/ABD was showing 900 base reads in this fashion at a recent user meeting. -Paul Paul Morrison Dana1030 Molecular Biology Core Facility Dana Farber Cancer Institute Boston, MA no connection to ABI aka PE/ABD ya da da, ya da da. From owner-software@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!ihnp4.ucsd.edu!news.service.uci.edu!buggus.mmg.uci.edu!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: PC GRAPHIC FILE FORMATS Followup-To: bionet.software Date: 6 May 1994 20:24:11 GMT Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 20 Distribution: world Message-ID: References: <9405061916.AA17394@gsbs18.gs.uth.tmc.edu> NNTP-Posting-Host: buggus.mmg.uci.edu In article <9405061916.AA17394@gsbs18.gs.uth.tmc.edu>, zharkikh@GSBS18.GS.UTH.TMC.EDU wrote: and if you want working code examples for most graphics formats (heavy on the unix, light on Mac and PC), try ftp.sdsc.edu in /pub/sdsc/graphics/imtools/[machine_architecture]/imtools || libsdsc You'd better be serious though, because there's about 11MB of code and src. You can del the binaries, of course because they won't be of any use on a PC, but the source also takes up a lot of space. SDSC usually does a good job on documenting it's code though, and there's a huge postscript doc file. -- Harry Mangalam, VCO/Micro+Mol Genetics, Irvine Hall, College of Medicine, UC Irvine, Irvine, CA, 92717, Vox:(714) 856-4824, Fax:(714) 725-2118, mangalam@uci.edu There's no better glory, when it all gets harried, to be laughing in the midst of it all. --- Doug and the Slugs --- From owner-software@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!ihnp4.ucsd.edu!news.service.uci.edu!buggus.mmg.uci.edu!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: reformatting gb/sp/pir retrievals Followup-To: bionet.software Date: 6 May 1994 20:13:08 GMT Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 31 Distribution: world Message-ID: References: <9405061812.AA04310@pines2.ljcrf.edu> NNTP-Posting-Host: buggus.mmg.uci.edu > Dear netters. > > I am looking for a way to reformat the documents I retrieve from genebank, swiss-protein or other databanks to either format accepted by ClustalV for example. The interfaces I have are Unix