From owner-embldatabank@net.bio.net Mon Apr 03 23:00:00 1995 Newsgroups: bionet.molbio.embldatabank From: Brendan@bphughes.demon.co.uk (Brendan P Hughes) Path: biosci!bcm!news.msfc.nasa.gov!sol.ctr.columbia.edu!howland.reston.ans.net!pipex!peernews.demon.co.uk!bphughes.demon.co.uk!Brendan Subject: TFASTA Unusual?? Organization: Myorganisation Reply-To: Moonshine@bothy.demon.co.uk X-Newsreader: Demon Internet Simple News v1.29 Lines: 43 X-Posting-Host: bphughes.demon.co.uk Date: Tue, 4 Apr 1995 18:27:40 +0000 Message-ID: <797020060snz@bphughes.demon.co.uk> Sender: usenet@demon.co.uk This note is a request for information and also an attempt to share what might be something of interest. My background in genomics is not good enough to say if this information is novel or is well established. I welcome your comments. As part of a project a cDNA was isolated for a particular binding protein. From time to time I searched the databases with the cDNA sequence to see if I could find homology with other sequences which might reveal a conserved motif for binding the particular ligand. Searches through EMBL and Genbank using FASTA were uninformative, they pulled a number of the homologous binding proteins across the various species. Eventually, I tried TFASTA. I ran the predicted peptide sequence of the binding protein against Gen:EMBL translated in all six reading frames. I got two hits-both very high quality. What was interesting was that both hits were from the biosynthetic enzyme for the ligand of the binding protein I was working with. Serendipity or a real biological significance?. I tried to align the nucleotide sequences of the hits with my cDNA but could find no match. Finally, after trying every possible combination, I tried aligning with opposite strands. This is where I had success-the hit on the biosynthetic gene was on a genomic sequence and the area of homology with the binding protein was in the 3' untranslated region of the synthetase. Starting with that last nucleotide on the 3' untranslated strand of the synthetase, the binding protein protein amino acid sequence was read off in two overlapping stretches. In all, there is 90% amino acid homology,and this is across species so with conservative substitution, this may be as high as a perfect match if I could use the homologous genomic sequences. However, they are not in the databases. Also interesting,the boundary of the two overlapping regions is marked by a peculiar motif. The overlapping stretches are in different reading frames. Is this unusual? Can anyone direct me to a reference which might explain the phenomenon (if it is such!). I have looked for intron/exon structure but the cDNA stretches are so close together it looks more like a reverse transcript Is this worth a note in one of the Genomics Journals? -- Brendan P Hughes -- s From owner-embldatabank@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!sunic.sunet.se!news.uni-c.dk!news.daimi.aau.dk!biobase!leslie From: leslie@biobase.dk (Leslie Olivier Johansen) Newsgroups: bionet.molbio.embldatabank Subject: Test! DO NOT READ Date: 4 Apr 1995 11:32:40 GMT Organization: The Danish BioBase Lines: 1 Message-ID: <3lraoo$l4u@biovax.biobase.dk> NNTP-Posting-Host: biobase.dk X-Newsreader: TIN [version 1.2 PL2] Sorry, I previously sent a test by mistake. From owner-embldatabank@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!pipex!sunic!sunic.sunet.se!news.uni-c.dk!news.daimi.aau.dk!biobase!leslie From: leslie@biobase.dk (Leslie Olivier Johansen) Newsgroups: bionet.molbio.embldatabank Subject: n Date: 4 Apr 1995 11:16:11 GMT Organization: The Danish BioBase Lines: 1 Message-ID: <3lr9pr$kgh@biovax.biobase.dk> NNTP-Posting-Host: biobase.dk X-Newsreader: TIN [version 1.2 PL2] From owner-embldatabank@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: roxanne@odin.mda.uth.tmc.edu (Roxanne Hall) Newsgroups: bionet.molbio.embldatabank Subject: A Protein Database Date: 4 Apr 1995 22:06:44 +0100 Lines: 20 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3lscd4$3ds@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk, genbankb@dl.ac.uk, embl-db@dl.ac.uk Can anyone refer me to a protein database or a database search utility which can select a protein based on the Molecular Weight and one other physical characteristic (i.e. the Isoelectric Point). Thank you in advance for your assistance. _____________________________________________________________________________ Roxanne Hall, Computer Programmer II ** In a world where there is so Biomathematics, University of Texas, ** much to be done, M.D. Anderson Cancer Center ** I feel strongly that there must 1515 Holcombe Blvd., MS 237, ** be something for me to do. Houston, Texas 77030 ** ** - Dorthea Dix E-Mail: roxanne@odin.mda.uth.tmc.edu ** Phone: 713/792-2604 From owner-embldatabank@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!oleane!jussieu.fr!univ-lyon1.fr!news From: duret@evoserv.univ-lyon1.fr.univ-lyon1.fr (Laurent Duret) Newsgroups: bionet.molbio.embldatabank Subject: Re: A Protein Database Date: 5 Apr 1995 06:31:57 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 34 Distribution: world Message-ID: <3ltdgt$r22@cismsun.univ-lyon1.fr> References: <3lscd4$3ds@mserv1.dl.ac.uk> Reply-To: duret@evoserv.univ-lyon1.fr.univ-lyon1.fr NNTP-Posting-Host: evoserv.univ-lyon1.fr In article 3ds@mserv1.dl.ac.uk, roxanne@odin.mda.uth.tmc.edu (Roxanne Hall) writes: > > > Can anyone refer me to a protein database or a database search utility > which can select a protein based on the Molecular Weight and one other > physical characteristic (i.e. the Isoelectric Point). > You can do this at the WWW Expasy Molecular Biology Server maintained by Amos Bairoch et al. in Geneva: http://expasy.hcuge.ch/www/expasy-top.html Go to "Tools" and then to "GuessProt" or directly go to: http://expasy.hcuge.ch/www/guess-prot.html Hope this helps, Laurent Duret ================================================================ Laurent Duret duret@biomserv.univ-lyon1.fr Tel: +33 72.44.81.42 Fax: +33 78.89.27.19 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 ================================================================ From owner-embldatabank@net.bio.net Tue Apr 11 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.embldatabank Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 12 Apr 1995 02:01:15 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 347 Sender: daemon@net.bio.net Distribution: world Message-ID: <199504120900.CAA07174@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. 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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 ASCB bionet.prof-society.ascb BIOCAN bionet.prof-society.cfbs 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 BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg BIO-WWW bionet.software.www CARDIOVASCULAR-RESEARCH bionet.biology.cardiovascular CELEGANS bionet.celegans CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CSM bionet.prof-society.csm CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMF-BIO bionet.emf-bio EMPLOYMENT bionet.jobs EMPLOYMENT-WANTED bionet.jobs.wanted FASEB bionet.prof-society.faseb GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses 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 MICROBIOLOGY bionet.microbiology MOLECULAR-EVOLUTION bionet.molbio.evolution MOLECULAR-MODELLING bionet.molec-model MOLLUSC-MOLECULAR-NEWS bionet.molbio.molluscs MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STADEN bionet.software.staden STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical URODELES bionet.organisms.urodeles VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast ZBRAFISH bionet.organisms.zebrafish 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-embldatabank@net.bio.net Mon Apr 17 23:00:00 1995 Path: biosci!rutgers!gatech!swrinde!cs.utexas.edu!news.sprintlink.net!psgrain!iafrica.com!ticsa.com!cstatd.cstat.co.za!ee.und.ac.za!quagga.ru.ac.za!caesar.wits.ac.za!pc16.med.wits.ac.za!075jon From: 075jon@chiron.wits.ac.za (Jonathan Patrick Burke) Newsgroups: bionet.molbio.embldatabank Subject: retrieve Date: Tue, 18 Apr 1995 08:42:16 GMT Organization: University of the witwatersrand Lines: 3 Message-ID: <075jon.8@chiron.wits.ac.za> NNTP-Posting-Host: pc16.med.wits.ac.za Keywords: PML, RARà, retrieve human and PML and RARà end From owner-embldatabank@net.bio.net Tue Apr 18 23:00:00 1995 Path: biosci!biosci!not-for-mail From: "Alexander J. Ropelewski" Newsgroups: bionet.molec-model,bionet.molbio.proteins,bionet.cellbiol,bionet.molbio.embldatabank,bionet.molbio.genbank,bionet.molbio.evolution,bionet.announce Subject: CCL:Sequence Analysis Workshop Date: 18 Apr 1995 17:59:59 -0700 Organization: Pittsburgh Supercomputing Center, Carnegie Mellon, Pittsburgh, PA Lines: 113 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: <0jZ0xSS00WB7FWtlVg@andrew.cmu.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molec-model:325 bionet.molbio.proteins:4323 bionet.cellbiol:2099 bionet.molbio.embldatabank:493 bionet.molbio.genbank:2010 bionet.molbio.evolution:2702 bionet.announce:2005 NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS Pittsburgh, Pennsylvania June 4-9, 1995 Pittsburgh Supercomputing Center (PSC) is again offering a five-day workshop on "Nucleic Acid and Protein Sequence Analysis," June 4-9, 1995. It is funded by a grant from the National Center for Human Genome Research of the National Institutes of Health. The workshop will familiarize biomedical researchers in applying supercomputing resources to problems of concern in macromolecular sequence analysis. Emphasis will be on alignment of and pattern extraction from multiple sequences. Participants will gain practical experience on PSC's Cray C-90 and T3D in (1) comparing and aligning sequences, (2) identifying informative patterns in a set of sequences; and (3) using extracted informative patterns to identify related sequences. Researchers will also learn several approaches to database searching and multiple sequence alignment, how to use profile analysis effectively, and how to identify patterns in their sequences. Participants are encouraged to bring sequence analysis problems from their current research. Extensive documentation will be given at the outset on the PSC computing environment as well as on the specific programs to be employed in the workshop. No prior supercomputing experience is required. Workshop leaders are Dr. Gary Churchill, Cornell University, Dr. Michael Gribskov, San Diego Supercomputing Center, and Dr. Hugh Nicholas, PSC. A limited number of grants to cover travel and hotel accommodations are available for U.S. academic participants. ALL PARTICIPANTS ARE REQUIRED TO PAY A $135 REGISTRATION FEE, IN ADVANCE, UPON ACCEPTANCE INTO THE WORKSHOP. DEADLINE FOR SUBMITTING APPLICATIONS IS FRIDAY, APRIL 21, 1995. Enrollment is lmited to 20 participants. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html * * * * * PITTSBURGH SUPERCOMPUTING CENTER NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS June 4-9, 1995 APPLICATION Name: ________________________________________________________________ Affiliation: ________________________________________________________________ Address: ________________________________________________________________ (Business) ________________________________________________________________ ________________________________________________________________ (Home) ________________________________________________________________ Telephone: ____________________________ ______________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_______________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) In order to attend the workshop, will you need funds for travel?___ lodging?___ Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:_________________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. If you have requested travel funds, please include the cost of roundtrip air fare from your home to Pittsburgh and indicate the amount of travel funds you will need. ALL PARTICIPANTS WILL BE REQUIRED TO PAY A $135 ADVANCE REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Please return all application materials by APRIL 21, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From owner-embldatabank@net.bio.net Fri Apr 28 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: mln Newsgroups: bionet.molbio.embldatabank Subject: crystallography position (fwd) Date: 29 Apr 1995 17:15:25 +0100 Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3ntomt$pkn@mserv1.dl.ac.uk> Original-To: embl-db@dl.ac.uk Dear Sir/Madam, I am a chemist- cum - crystallographer. Looking for a suitable position in a research laboratory. Those who have positions available may please ask for cv/biodata. Research Interest: Crystallography (Macromolecular/small molecular) drug designing molecular modelling bioinformatics /Protein,DNA structure analysis expecting an earlier response thanking you sincerely yours M. Lakshmi Narayanan