From owner-bio-matrix@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.molbio.bio-matrix Subject: IMPORTANT BIOSCI INFORMATION Message-ID: <9310080900.AA21872@net.bio.net> Date: 8 Oct 93 09:00:04 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 243 Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS and waismail access (waismail is our WAIS e-mail server, more below) and will also be available for access via other gopher sites if they wish to permit it. The raw unindexed data is available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.welch.jhu.edu and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIO-SOFTWARE bionet.software CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-bio-matrix@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!uwm.edu!rpi!mantell From: mantell@alum01.its.rpi.edu (Abraham S. Mantell) Newsgroups: bionet.molbio.bio-matrix Subject: Books for Sale Message-ID: <294ucu$fcd@usenet.rpi.edu> Date: 8 Oct 93 23:50:54 GMT Organization: Rensselaer Polytechnic Institute, Troy NY Lines: 32 NNTP-Posting-Host: alum01.its.rpi.edu Hello, I found a few more books of mine that I wish to sell... 1. Chemical Synthesis in Molecular Biology: Biological Macromolecules with Natural and Modified Monomer Units, From a Symposium held in Brauschweig, FRG, September 1984. Ed. by Blocker, Frank, and Fritz. 1987, softcover. List Price: $105 I ask: $70 2. Flux Coordinates and Magnetic Field Structure: A Guide to a Fundamental Tool of plasma theory, by D'haeseleer, Callen, and Shohet, 1991, Springer-Verlag. List Price: $98 I ask: $70 3. Elliptic Curves, by Dale Husemoller, 1987, Springer-Verlag GTM v.111. List Price: $49 I ask: $30 4. Series of Irregular Observations: Forecasting and Model Building, by Azencott and Dacunha-Castelle, 1986. List Price: $46 I ask: $30 Please add a few dollars for postage, insurance, and COD (if used). All books are in like-new condition... Abe mantell@rpi.edu From owner-bio-matrix@net.bio.net Sun Oct 10 23:00:00 1993 Path: biosci!uwm.edu!rpi!mantell From: mantell@alum01.its.rpi.edu (Abraham S. Mantell) Newsgroups: bionet.molbio.bio-matrix Subject: Books for Sale Message-ID: <294ucu$fcd@usenet.rpi.edu> Date: 8 Oct 93 23:50:54 GMT Organization: Rensselaer Polytechnic Institute, Troy NY Lines: 32 NNTP-Posting-Host: alum01.its.rpi.edu Hello, I found a few more books of mine that I wish to sell... 1. Chemical Synthesis in Molecular Biology: Biological Macromolecules with Natural and Modified Monomer Units, From a Symposium held in Brauschweig, FRG, September 1984. Ed. by Blocker, Frank, and Fritz. 1987, softcover. List Price: $105 I ask: $70 2. Flux Coordinates and Magnetic Field Structure: A Guide to a Fundamental Tool of plasma theory, by D'haeseleer, Callen, and Shohet, 1991, Springer-Verlag. List Price: $98 I ask: $70 3. Elliptic Curves, by Dale Husemoller, 1987, Springer-Verlag GTM v.111. List Price: $49 I ask: $30 4. Series of Irregular Observations: Forecasting and Model Building, by Azencott and Dacunha-Castelle, 1986. List Price: $46 I ask: $30 Please add a few dollars for postage, insurance, and COD (if used). All books are in like-new condition... Abe mantell@rpi.edu From owner-bio-matrix@net.bio.net Wed Oct 20 23:00:00 1993 Path: biosci!SCRI.FSU.EDU!STRELETS From: STRELETS@SCRI.FSU.EDU Newsgroups: bionet.molbio.bio-matrix Subject: Announcement: new gene (exon/intron) revealing system for PC Message-ID: <931021090020.2060a665@scri.fsu.edu> Date: 21 Oct 93 13:00:20 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 163 SAGITTARIUS DNA Block Marker **************************** SAGITTARIUS DNA Block Marker is a package for exon/intron structure revealing on the base of protein k-tuples statistic, with orientation on MS DOS PC-compartibles (386 or 486 recommended). Input: any sequence file (.SEQ). Probably (not well tested..) you can use free format sequence representation, GCG-style files, standard sequence extractions from GENBANK or EMBL databases etc. Output: on-screen and in file EXONS.RES. Output includes probable coding regions list (start-end, frame#, weight) with corresponding aminoacid sequences (this is special feature of this method - even in the case of nonperfect region boundary prediction error in coding frame is practically impossible), and suggested variant of assembled gene sequence (start-end and frame# for all included regions) with full coded aminoacid sequence. Alternative input: in presense of SAGITTARIUS GENBANK on your computer you can use on input any file with bank numbers (.NOM, standard output of buffer content from SAGITTARIUS databanks). Program will predict coding regions and genes for corresponding database sequences in parallel with demonstration of real GENBANK CDS features for each sequence what allows to test prediction quality on the set of well-known genes (learning mode). In the case of user sequence input (from file .SEQ) program will search for coding regions in both of direct and inverted strands consequently (independent predictions). ------------------------------------------------------------- Short algorithm description --------------------------- Taking into accout a certain proximity of the k-tuple (peptide) organization of proteins with similar structure and/or functions, a new method is proposed for detection of coding regions of genome based on mapping of newly sequenced DNA regions by subsequences "admissibility" function. This function obtained by k-tuple analysis of protein data base. In the simplest case, this algorithm marks all the k-tuples not found in real proteins as structural prohibitions which are forbidden in the coding regions of analogous proteins. The longest regions without such prohibitions can be realized as the best exon (for eukaryotic genome) or active gene (for prokaryotic genome). To ensure a statistically significant level in the comparison of different sequences, the length k of the used k-tuples is chosen taking into account the general incidence of respective peptides in the data base. Thus, for chance sequences with the same amino acid composition as the data base under study, all the used k-tuples must be realized in the data base at least once. In this case, the absence of some k-tuples can detect both the limitations on the primary protein structure and a mere lack of statistical data. The proposed algorithm has been tested on the basis of the latest releases of data bases EMBL and SwissProt. As the best examples, human genes with a complicated exon/intron structures were tested. Practically in all cases, the longest region without any k-tuple prohibitions was present in the database EMBL as CDS feature. For all the other shorter real exons, the same result was observed, although with a lower signal/noise ratio. The position forecast for the longest exon was much higher than in the case of using other coding potentials (up to 95% instead of 60-70%). The field of application of the proposed algorithm is somewhat limited by the existence of a structural or functional analog of the coded protein among the already sequenced proteins in the data base. The probability of such a failure has been estimated by means of checking the number of appearing new superfamily proteins in two consecutive releases of PIR base and found to be 2-5%. In all other cases the algorithm may be used as a tool for a rapid and accurate detection of at least one best exon in a eukaryotic genome (with subsequent more detailed study of complete exon structure by means of usual algorithms) or a complete active gene in a prokaryotic one. ------------------------------------------------------------- SAGITTARIUS DNA Block Marker is available by anonymous FTP from: - FTP.SCRI.FSU.EDU, directory /pub/genetics/exons/ Probably SAGITTARIUS DNA Block Marker is available by anonymous FTP from some of the well-known bio-servers (iubio etc.). ------------------------------------------------------------- Installation ------------ Distributive variant includes ready-for-use informational files and executables (2.5 Mb in total) - all in self-extracting archieve (file exonsall.exe). All decompressed SAGITTARIUS DNA Block Marker files must be placed in one directory (including Borland .BGI and huge .WRK files). Program intensively read data from huge file .WRK what slow down prediction process. If you have on your computer virtual (in-memory) disk of at least 2.1 Mb capasity you may copy huge file .WRK on this disk before program running and assign this disk drive letter G:. Such operation allows program to find .WRK file copy on this (G:) virtual disk and speed up process at least 5 times. In absense of such large virtual disk program will use .WRK file from current directory. -------------------------------------------------------------- SAGITTARIUS is a FREE DOMAIN software. This package (with compressed data files) can be redistributed freely without any limitations but only free of charge and for non-commercial usage. No changes in data files and/or executables allowed. -------------------------------------------------------------- For HELPFUL comments and discussions please contact: Dr. Victor B.Strelets (strelets@scri.fsu.edu) or Dr. Hwa A.Lim (hlim@scri.fsu.edu) Supercomputer Computations Research Institute, Florida State University, B-186, Tallahassee, FL 32306-4052, USA --------------------------------------------------------------- Common SAGITTARIUS information ------------------------------ SAGITTARIUS is a family of free domain application packages for molecular biologists with orientation on MS DOS PC-compartibles: - Compressed sequence databases with dialog shells for fast and easy data manipulation (PIR and GENBANK variants) - Fast programs for cross-bank user SEQ homology searches (short subregion homologies sensitive) (closely connected with compressed SAGITTARIUS databases) - Fast sensitive programs for pairwaise alignments (both aminoacid and nucleotide), including cross-bank user SEQ alignments (closely connected with compressed databases to allow cross-bank user SEQ alignments) - Packages for fast tree-based multiple alignments - Package for sequenation-errors-stable contigs joining (on the base of tree-based multiple alignment) - Automated system for revealing coding regions (exon/intron structure) in new nucleotide sequences (including learning mode access to the nucleotide sequences in compressed SAGITTARIUS GENBANK database) - Personal Reference Database dialog shell for manipulation of data from standard BIO-JOURNALS(BIOSCI), SEQANALREF(Bairoch), JOURNALS-TOC(multiple sources) databases -------------------------------------------------------------- Author(s) will in no way be held liable for any loss of profit or any other commercial damage including but not limited to special, incidental, consequential or other damages from use of this package. You may use them only with the understanding that you use it at your own risk and that your use of the software is your agreement to this disclaimer. From owner-bio-matrix@net.bio.net Fri Oct 22 23:00:00 1993 Path: biosci!CBIL.HUMGEN.UPENN.EDU!coverton From: coverton@CBIL.HUMGEN.UPENN.EDU (Chris Overton) Newsgroups: bionet.molbio.bio-matrix Subject: references on bio DB integration Message-ID: <9310231648.AA08342@cbil.humgen.upenn.edu> Date: 23 Oct 93 16:48:56 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 23 I'm looking for references to work describing the integration of multiple biological databases (well >= 2 at least). I'm interested in examples where a federated schema was developed that supports multi-database queries. I'm especially interested in examples of distributed database systems with a federated schema. However, I'll take any and all references to systems that support multi-database queries. Examples of types of systems: 1 -- Uniform interface to multiple databases. 2 -- Monolithic database containing multiple, independent, unintegrated schemas. 3 -- Monolithic database containing multiple, integrated schemas (federated). 4 -- Distributed database system without federated schema. 5 -- Distributed database system with federated schema. etc. Thanks for your help. Chris Overton From owner-bio-matrix@net.bio.net Mon Oct 25 22:00:00 1993 Path: biosci!IME.UNICAMP.BR!sonia From: sonia@IME.UNICAMP.BR (Sonia Elena Palomino Castro - POS_MAP) Newsgroups: bionet.molbio.bio-matrix Subject: (none) Message-ID: <9310262023.AA09361@uxime16.ime.unicamp.br> Date: 26 Oct 93 22:23:58 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 1 unsubscribe biomatrix From owner-bio-matrix@net.bio.net Tue Oct 26 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!paladin.american.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!rpi!ghost.dsi.unimi.it!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!sun.rediris.es!power.ci.uv.es!evalun11!balbuena From: BALBUENA@EVALUN11.BITNET Newsgroups: bionet.molbio.bio-matrix Subject: Re: (none) Message-ID: <93300.103303BALBUENA@EVALUN11.BITNET> Date: 27 Oct 93 15:33:03 GMT References: <9310262023.AA09361@uxime16.ime.unicamp.br> Distribution: bionet Organization: Valencia University (Universitat de Valencia) SPAIN Lines: 8 Please unsubscribe me. Sorry for sending this to the list but all attempts to sign off failed. Juan A. Balbuena Department of Animal Biology, University of Valencia, Spain. phone: +34 6 386 43 75 fax: +34 6 386 43 72 e-mail: balbuena@vm.ci.uv.es or BALBUENA@EVALUN11.BITNET