From owner-embldatabank@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!biosci!not-for-mail From: "Alexander J. Ropelewski" Newsgroups: bionet.announce,bionet.molbio.proteins,bionet.molbio.embldatabank,bionet.molbio.genbank,bionet.molbio.evolution,sci.research,sci.bio.technology Subject: Sequencing Analysis workshop Annoucement Date: 2 Mar 1995 14:17:48 -0800 Organization: Pittsburgh Supercomputing Center, Carnegie Mellon, Pittsburgh, PA Lines: 114 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:1861 bionet.molbio.proteins:3876 bionet.molbio.embldatabank:460 bionet.molbio.genbank:1962 bionet.molbio.evolution:2508 sci.research:4024 sci.bio.technology:2392 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 with computational methods and provide practice 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. The deadline for submitting applications is April 17, 1995. Enrollment is limited 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 $135 ADVANCE REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Please return all application materials by APRIL 17, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From owner-embldatabank@net.bio.net Fri Mar 03 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!uunet!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: fniner@aol.com (FNINER) Newsgroups: bionet.molbio.embldatabank Subject: Accession numbers for human JAKs and STATs Date: 4 Mar 1995 06:27:01 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 7 Sender: root@newsbf02.news.aol.com Message-ID: <3j9iq5$rqv@newsbf02.news.aol.com> Reply-To: fniner@aol.com (FNINER) NNTP-Posting-Host: newsbf02.mail.aol.com I am interested in obtaining nucleotide sequences for HUMAN Janus family of protein tyrosine kinases (JAK1, JAK2, JAK3, and Tyk2) and also various HUMAN Signal Transducers and Activators of Transcription (STAT1 - STAT6) proteins. I would greatly appreciate any information concerning the accession numbers for these genes. Many thanks in advance. FNINER@AOL.COM From owner-embldatabank@net.bio.net Fri Mar 03 22:00:00 1995 Newsgroups: bionet.molbio.embldatabank Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: Re: Accession numbers for human JAKs and STATs Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Sat, 4 Mar 1995 17:56:12 GMT References: <3j9iq5$rqv@newsbf02.news.aol.com> Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 94 FNINER (fniner@aol.com) wrote: : I am interested in obtaining nucleotide sequences for HUMAN Janus family : of protein tyrosine kinases (JAK1, JAK2, JAK3, and Tyk2) and also various : HUMAN Signal Transducers and Activators of Transcription (STAT1 - STAT6) : proteins. I would greatly appreciate any information concerning the : accession numbers for these genes. Many thanks in advance. : FNINER@AOL.COM If you have access to Mosaic or Netscape, you can easily answer this question yourself. The Sequence retrieval system (SRS) servers allow you to select information from a wide range of sequence and sequence related databases. There are several SRS Servers, I describe here how to work with the EBI one Except for the URL, the other will work similarly Access the following URL: http://www.ebi.ac.uk/srs/srsc or http://www.ebi.ac.uk select [database query/retrieval] select [Sequence Retrieval System] select [search sequence libraries] select the database(s) you want to search, type in the keywords of interest and select [do-query] I selected embl+emnew and the following keywords: Definition: JAK Organism: homo Alltext: tyrosine which gave me: ID HS09607 standard; RNA; PRI; 4064 BP. XX AC U09607; XX DT 14-JUL-1994 (Rel. 40, Created) DT 14-JUL-1994 (Rel. 40, Last updated, Version 1) XX DE Human JAK family protein tyrosine kinase (JAK3) mRNA, complete cds. ... D HSPTKJAK standard; RNA; PRI; 3541 BP. XX AC M64174; M35203; XX DT 12-APR-1991 (Rel. 28, Created) DT 20-JAN-1993 (Rel. 34, Last updated, Version 2) XX DE Human protein-tyrosine kinase (JAK1) mRNA, complete cds. XX ... ID HS76112 standard; RNA; EST; 321 BP. XX AC T29761; XX DT 09-JAN-1995 (Rel. 42, Created) DT 09-JAN-1995 (Rel. 42, Last updated, Version 1) XX DE EST93948 Homo sapiens cDNA 5' end similar to tyrosine kinase JAK1 DE (HT:92). XX ... Exchanging TYK for JAK, gave XX AC X54637; XX DT 05-NOV-1990 (Rel. 25, Created) DT 12-SEP-1993 (Rel. 36, Last updated, Version 2) XX DE Human tyk2 mRNA for non-receptor protein tyrosine kinase XX KW protein tyrosine kinase. I leave the query with the STAT's to you, I do not want to take all the fun out of it :-) -- Jeroen ====================================================================== . O . Jeroen Coppieters . O O o O . Software Support O O O O *o O O Jeroen.Coppieters@ebi.ac.uk O O O O( *o )O O ++44 1223 494422 )O O O O o* O O( O O O O( o* )O O )O O O O *o O O( EMBL Outstation EBI O O O O( *o )O O (European Bioinformatics Institute) )O @ O O o* O O( Hinxton Hall O O O( o* )O(' Hinxton ` O( *o O ' Cambridge CB10 1RQ ` O ' UK http://www.ebi.ac.uk ====================================================================== From owner-embldatabank@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!genetics.com!mcolbert From: mcolbert@genetics.com Newsgroups: bionet.molbio.embldatabank Subject: ftp site for full release of EMBL Date: 6 Mar 1995 11:02:36 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503061857.AA21933@genetics.com> NNTP-Posting-Host: net.bio.net Hello, I would like to know where there is an anonymous ftp site for the latest full release of EMBL. I am on the east coast of the U.S. I know where the updates are located. Thanks. -Maureen Colbert mcolbert@genetics.com From owner-embldatabank@net.bio.net Tue Mar 07 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!swiss.ans.net!paperboy.amoco.com!cronkite!usenet From: wmmounts@amoco.com (Bill Mounts) Newsgroups: bionet.molbio.embldatabank Subject: SWISS-PROT File Formats... Date: 8 Mar 1995 16:54:39 GMT Organization: Amoco Corporation Lines: 11 Message-ID: <3jkngf$60f@cronkite.amoco.com> Reply-To: wmmounts@amoco.com I am looking for definitions of the following of the following line codes which are currently in use with the SWISS-PROT database. Any help is greatly appreciated. GN RP RC RM Thanks again... Bill From owner-embldatabank@net.bio.net Thu Mar 09 22:00:00 1995 Newsgroups: bionet.molbio.embldatabank Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!EU.net!Belgium.EU.net!idefix.CS.kuleuven.ac.be!reks.uia.ac.be!news From: bone@reks.uia.ac.be (Darth Vader) Subject: Re: IMPORTANT OPPORTUNITY Message-ID: <1995Mar10.082301.11869@reks.uia.ac.be> Sender: news@reks.uia.ac.be (USENET News System) Organization: University of Antwerp X-Newsreader: Date: Fri, 10 Mar 1995 08:23:01 GMT Lines: 2 ..maybe we should ask mafia for a protection against bitch like that and any other idiot that puts a message scoring more than 90 on the bullshit meter? From owner-embldatabank@net.bio.net Thu Mar 09 22:00:00 1995 Newsgroups: bionet.software,bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!newsxfer.itd.umich.edu!zip.eecs.umich.edu!caen!hearst.acc.Virginia.EDU!murdoch!reed0.med.Virginia.EDU!wrp From: wrp@reed0.med.Virginia.EDU (Bill Pearson) Subject: FASTA 2.0x avaiable X-Nntp-Posting-Host: reed0.med.virginia.edu Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia Date: Fri, 10 Mar 1995 15:45:29 GMT Lines: 41 Xref: biosci bionet.software:11426 bionet.molbio.genbank:1970 bionet.molbio.embldatabank:467 bionet.molbio.proteins:3942 A new (experimental) release of the FASTA program package is now available from virginia.edu in pub/fasta/fasta20x.shar(.Z). Version 2.0x incorporates several major improvements in the FASTA and SSEARCH (Smith-Waterman) sequence searching programs: (1) Explicit statistical estimates are now available from FASTA, TFASTA, and SSEARCH. Expectation values (a la BLAST) are provided for library similarity scores. In addition, raw similarity scores are normalized to correct for the expected length-dependence of similarity scores. The statistical estimates are very accurate for SSEARCH and for FASTA if the "-o" option is used. The "-o" option improves dramatically the performace of FASTA - at a cost in execution time - I recommend strongly that you use it as often as possible for proteins. For DNA it serves no purpose. (2) FASTA now uses the rigorous Smith-Waterman algorithm to produce alignments. Thus, there is no limit to length size in alignments. (3) The BLOSUM50 matrix is now used by default. (4) It is easy to change the penalties for the first residue (now -12 by default) and additional residue (-2) in a a gap. (5) A new alignment option "-m 4", makes it easy to display the part of the query sequence that is aligned to the library sequence. For many protein families, one expects for the alignment to extend from one end of the sequence to the other. This display makes it easy to see when the alignments become much shorter. This version has only been tested for a few weeks, thus the version number 2.0x. Please let me know if you have any problems with it. Bill Pearson wrp@virginia.edu -- wrp@virginia.EDU Dept. of Biochemistry #440 U. of Virginia Charlottesville, VA 22908 From owner-embldatabank@net.bio.net Fri Mar 10 22:00:00 1995 Newsgroups: bionet.software,bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.proteins Path: biosci!rutgers!rockyd!notes From: "Dr. Kent L. Nastiuk" Subject: Re: FASTA 2.0x avaiable X-Nntp-Posting-Host: nastiuk_pc.rockefeller.edu Message-ID: Sender: notes@rockyd.rockefeller.edu (News Administrator) Organization: Rockefeller University References: Date: Sat, 11 Mar 1995 18:53:47 GMT Lines: 14 Xref: biosci bionet.software:11437 bionet.molbio.genbank:1973 bionet.molbio.embldatabank:470 bionet.molbio.proteins:3952 wrp@reed0.med.Virginia.EDU (Bill Pearson) wrote: > > > A new (experimental) release of the FASTA program package is now > available from virginia.edu in pub/fasta/fasta20x.shar(.Z). Version > 2.0x incorporates several major improvements in the FASTA and SSEARCH > (Smith-Waterman) sequence searching programs: > i tried to login to 'virginia.edu' and 'reed0...', but could access neither could you provide better ftp site information, including how to login (ie guest, anonymous, or whatever? thanks From owner-embldatabank@net.bio.net Fri Mar 10 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news2.near.net!das-news2.harvard.edu!oitnews.harvard.edu!hsdndev!purdue!mozo.cc.purdue.edu!macg203d.bio.purdue.edu!user From: shall@bilbo.bio.purdue.edu (Stephen Hall) Newsgroups: bionet.molbio.embldatabank Subject: Re: IMPORTANT OPPORTUNITY Date: Sat, 11 Mar 1995 14:40:21 -0800 Organization: Purdue University Lines: 12 Message-ID: References: <1995Mar10.082301.11869@reks.uia.ac.be> NNTP-Posting-Host: macg203d.bio.purdue.edu In article <1995Mar10.082301.11869@reks.uia.ac.be>, bone@reks.uia.ac.be (Darth Vader) wrote: > ..maybe we should ask mafia for a protection against bitch like that and any > other idiot that puts a message scoring more than 90 on the bullshit meter? One responded that this type of posting that Vader refers to is evidence that brothers and sisters shouldn't mate. But people like Mr. Haythorn, one of the originators of this posting, and their families have worked at inbreeding for many generations. I mean they should feel a real sense of accomplishment that they have managed to bring the recessive mutation for idiocy into the homozygous state. From owner-embldatabank@net.bio.net Fri Mar 10 22:00:00 1995 Path: biosci!biosci!not-for-mail From: Bill Pearson Newsgroups: bionet.software,bionet.molbio.embldatabank,bionet.molbio.genbank,bionet.announce,bionet.molbio.proteins Subject: FASTA 2.0x available Date: 11 Mar 1995 07:30:55 -0800 Organization: University of Virginia Lines: 40 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:11434 bionet.molbio.embldatabank:468 bionet.molbio.genbank:1972 bionet.announce:1887 bionet.molbio.proteins:3949 A new (experimental) release of the FASTA program package is now available from virginia.edu in pub/fasta/fasta20x.shar(.Z). Version 2.0x incorporates several major improvements in the FASTA and SSEARCH (Smith-Waterman) sequence searching programs: (1) Explicit statistical estimates are now available from FASTA, TFASTA, and SSEARCH. Expectation values (a la BLAST) are provided for library similarity scores. In addition, raw similarity scores are normalized to correct for the expected length-dependence of similarity scores. The statistical estimates are very accurate for SSEARCH and for FASTA if the "-o" option is used. The "-o" option improves dramatically the performace of FASTA - at a cost in execution time - I recommend strongly that you use it as often as possible for proteins. For DNA it serves no purpose. (2) FASTA now uses the rigorous Smith-Waterman algorithm to produce alignments. Thus, there is no limit to length size in alignments. (3) The BLOSUM50 matrix is now used by default. (4) It is easy to change the penalties for the first residue (now -12 by default) and additional residue (-2) in a a gap. (5) A new alignment option "-m 4", makes it easy to display the part of the query sequence that is aligned to the library sequence. For many protein families, one expects for the alignment to extend from one end of the sequence to the other. This display makes it easy to see when the alignments become much shorter. This version has only been tested for a few weeks, thus the version number 2.0x. Please let me know if you have any problems with it. Bill Pearson wrp@virginia.edu -- wrp@virginia.EDU Dept. of Biochemistry #440 U. of Virginia Charlottesville, VA 22908 From owner-embldatabank@net.bio.net Sat Mar 11 22:00:00 1995 Newsgroups: bionet.software,bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.proteins Path: biosci!lhc!borduas!francis From: francis@borduas.nlm.nih.gov (Francis Ouellette) Subject: Re: FASTA 2.0x avaiable Message-ID: <1995Mar12.220021.15425@nlm.nih.gov> Followup-To: bionet.software,bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.proteins Sender: news@nlm.nih.gov Organization: National Library of Medicine X-Newsreader: TIN [version 1.2 PL2] References: Date: Sun, 12 Mar 95 22:00:21 GMT Lines: 50 Xref: biosci bionet.software:11444 bionet.molbio.genbank:1974 bionet.molbio.embldatabank:471 bionet.molbio.proteins:3956 Dr. Kent L. Nastiuk (nastiuk@rockvax.rockefeller.edu) wrote: > wrp@reed0.med.Virginia.EDU (Bill Pearson) wrote: > > > > > > A new (experimental) release of the FASTA program package is now > > available from virginia.edu in pub/fasta/fasta20x.shar(.Z). Version > > 2.0x incorporates several major improvements in the FASTA and SSEARCH > > (Smith-Waterman) sequence searching programs: > > > i tried to login to 'virginia.edu' and 'reed0...', but could access neither > could you provide better ftp site information, including how to login > (ie guest, anonymous, or whatever? If you look in Amos Bairoch's 'serv_ftp.txt' document, you will find these coordinates (login anonymous, use your e-mail address as password. -------------------------------------------------------------------- Organiz.: University of Virginia / USA Address : uvaarpa.virginia.edu (128.143.2.7) Programs: Name=FASTA; Desc=database search program; OS=UNIX and DOS; Directory= /pub/fasta Contact : William Pearson; wrp@virginia.edu Status : Tested (30 Sep 1992). -------------------------------------------------------------------- I went to check, and all the files where in the right place ... so if Amos sees this mail, he can update the 'Status' to >> Status : Tested (12 Mar 1995). The latest version of Amos' document is available by anonymous FTP from expasy.hcuge.ch (IP address 129.195.254.61) in the /database/info directory as 'serv_ftp.txt'. This (and many others) is also available from the WWW at this URL: http://expasy.hcuge.ch/info/serv_ftp.txt regards, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov From owner-embldatabank@net.bio.net Sat Mar 11 22:00:00 1995 Newsgroups: bionet.molbio.embldatabank Path: biosci!lhc!borduas!francis From: francis@borduas.nlm.nih.gov (Francis Ouellette) Subject: Re: SWISS-PROT File Formats... Message-ID: <1995Mar12.222054.15798@nlm.nih.gov> Sender: news@nlm.nih.gov Organization: National Library of Medicine X-Newsreader: TIN [version 1.2 PL2] References: <3jkngf$60f@cronkite.amoco.com> Date: Sun, 12 Mar 95 22:20:54 GMT Lines: 58 Bill Mounts (wmmounts@amoco.com) wrote: > I am looking for definitions of the following of the following > line codes which are currently in use with the SWISS-PROT > database. Any help is greatly appreciated. > GN > RP > RC > RM Bill, if you at the swiss-prot user manual you will find the information below (and lots more too) regards, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov Each line begins with a two-character line code, which indicates the type of data contained in the line. The current line types and line codes and the order in which they appear in an entry, are shown below: ID - Identification. AC - Accession number(s). DT - Date. DE - Description. GN - Gene name(s). OS - Organism species. OG - Organelle. OC - Organism classification. RN - Reference number. RP - Reference position. RC - Reference comments. RM - Reference Medline. RA - Reference authors. RL - Reference location. CC - Comments or notes. DR - Database cross-references. KW - Keywords. FT - Feature table data. SQ - Sequence header. - (blanks) sequence data. // - Termination line. rest of document available from: http://expasy.hcuge.ch/txt/userman.txt From owner-embldatabank@net.bio.net Sun Mar 12 22:00:00 1995 Newsgroups: bionet.molbio.genome-program,bionet.molbio.embldatabank,embnet.general Path: biosci!agate!howland.reston.ans.net!pipex!oleane!jussieu.fr!citi2.fr!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: an EMBL gopher Message-ID: <1995Mar12.085904.8295@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: Date: Sun, 12 Mar 1995 08:59:04 GMT Lines: 54 Xref: biosci bionet.molbio.genome-program:1261 bionet.molbio.embldatabank:473 G. Giacomo Consalez (consaleg@dibit.hsr.it) wrote: : I have been looking for a functioning EMBL gopher server to retrieve : genembl and genpept entries, just like I regularly do for genbank, : swissprot and PIR entries. None seems to be running. A www server would be : fine, although gopher products are much faster. To my knowledge, we run the only database gopher on EMBL and EMBL updates world-wide. There are on average more than 300 requests served per day. Peak requests are more than 1200 daily which is due to some unfortunate ambition to run automaitc scripts. There are two issues to be kept in mind. (1) The server runs on an Indigo3000, which is the same machine which we introduced the service on in 1992. This machine runs brilliantly but deserves a major CPU and memory upgrade which is unfortunately unrealistic for such a service. Updating GOPHER indices is a pretty resource-consuming step. We currently need more than an hour to create the waisindex. If you apprach the server at that time you will get rejected. Depending on load, it can take up to a minute if you do get a result in peak hours. (2) WAIS-indexing is a full-text search. This means that a full text is analyzed for keywords. The more keywords there are the slower WAIS will become. Worse, it will not allow searches for trivial words ('protein', 'mrna') as it has a built-in limitation to not incorporate words occuring more than a given number. : Anybody with a good suggestion? Use the WWW-based SRS browser from Thure Etzold; on many EMBnet nodes, including the one in Bari, you'll find local versions also. http://www.embl-heidelberg.de/srs/status.html is the overview on the available SRS servers on the network. : Thanks. Question for the community: How long will this service need to run? Despite the disk space resources the machine which it is running on has been frozen in its OS. The code has been modified to an extend which makes it highly questionable whether it will ever run on a more advanced OS version. This implies that, if the box dies, the service will die as well with short notice. Would you bother? Regards Reinhard Doelz EMBnet Switzerland -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-embldatabank@net.bio.net Sun Mar 12 22:00:00 1995 Newsgroups: bionet.molbio.embldatabank,embnet.general Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!pipex!oleane!jussieu.fr!citi2.fr!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: an EMBL gopher Message-ID: <1995Mar12.100054.9038@comp.bioz.unibas.ch> Followup-To: bionet.molbio.embldatabank,embnet.general Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <1995Mar12.085904.8295@comp.bioz.unibas.ch> Date: Sun, 12 Mar 1995 10:00:54 GMT Lines: 78 Reinhard Doelz (doelz@comp.bioz.unibas.ch) wrote: : (2) WAIS-indexing is a full-text search. This means that a full : text is analyzed for keywords. The more keywords there are : the slower WAIS will become. Worse, it will not allow searches : for trivial words ('protein', 'mrna') as it has a built-in : limitation to not incorporate words occuring more than a given : number. Colleagues, to give you an example, look at the xembl index and see that the following words are affected (about 300). This is not a real word but a phenomenon caused by not merging the index block of this word. (xembl is only the daily updates. Real 'embl' has a much higher exclusion rate.) adams, adamskerlavage, animalia, animaliametazoa, assessment, based, basedupon, basepairs, bednarik, bednarikcao, blake, blakebrandon, bp, brandon, brandonchiu, bult, bultlee, cao, caocepeda, catarrhini, catarrhinihominidae, cdna, cepeda, cepedacoleman, chiu, chiuclayton, chordata, chordatavertebrata, clark, clarkdubuque, clayton, claytoncline, cline, clinecotton, clone, coleman, colemancollins, collins, collinsdimke, cotton, cottonearle, dillon, dillonfannon, dimke, dimkefeng, diversity, dubuque, dubuqueelliston, earle, earlehughes, elliston, ellistonhawkins, est, esthomo, estproject, eukaryota, eukaryotaanimalia, eukaryotaplantae, eutheria, eutheriaprimates, expression, expressionpatterns, fannon, fannonrosen, feng, fengferrie, ferrie, ferriefischer, fields, fieldsfraser, fine, finefitzgerald, fischer, fischerhastings, fitzgerald, fitzgeraldfitzhugh, fitzhugh, fitzhughfritchman, fleischmanfuldner, fleischmann, fragment, fraser, fraserventer, fritchman, fritchmangeoghagen, fuldner, fuldnerbult, gene, genediversity, genexpress, genexpressgenexpress, genexpressthe, geoghagen, geoghagenglodek, glodek, glodekgnehm, gnehm, gnehmhanna, gocayne, gocaynewhite, greene, greenegruber, gruber, gruberhudson, hanna, hannahedblom, haplorhini, haplorhinicatarrhini, haseltine, haseltinefields, hastings, hastingshe, hawkins, hawkinsholman, hedblom, hedblomhinkle, hehu, hillier, hillierclark, hinkle, hinklejr, holman, holmanhultman, hominidae, hominidaeadams, hominidaegenexpress, hominidaehillier, homo, hu, hudson, hudsonkim, hughes, hughesfine, hugreene, hultman, hultmankucaba, human, humangene, initial, initialassessment, ji, jili, jr, jrkelley, kelley, kelleyklimek, kelleyliu, kerlavage, kerlavagefleischman, kim, kimkozak, kirkness, kirknessweinstock, klimek, klimekkelley, kozak, kozakkunsch, kucaba, kucabale, kunsch, kunschji, le, lee, leekirkness, lelennon, lennon, lennonmarra, li, libednarik, limeissner, liu, liumarmaros, mammalia, mammaliatheria, marmaros, marmarosmerrick, marra, marraparsons, mcdonald, mcdonaldnguyen, meissner, meissnerolsen, merck, merckest, merrick, merrickmoreno, metazoa, metazoachordata, millionbasepairs, moreno, morenopalanques, nguyen, nguyenpellegrino, olsen, olsenraymond, palanques, palanquesmcdonald, parsons, parsonsrifkin, partial, patterns, patternsbased, pellegrino, pellegrinophillips, phillips, phillipsryder, plantae, primates, primateshaplorhini, program, project, raymond, raymondwei, rifkin, rifkinrohlfing, rna, rnaest, rohlfing, rohlfingtan, rosen, rosenhaseltine, ruben, rubendillon, ryder, ryderscott, sapiens, saudek, saudekshirley, scott, scottsaudek, sequence, shirley, shirleysmall, similar, small, smallspriggs, spriggs, spriggsutterback, standard, sutton, suttonblake, tan, tantrevaskis, thegenexpress, theria, theriaeutheria, transcribed, trevaskis, trevaskiswaterston, utterback, utterbackweidman, venter, venterinitial, vertebrata, vertebratamammalia, washu, washumerck, waterston, waterstonwilliamson, wei, weidman, weidmanli, weinstock, weinstockgocayne, weiwing, white, whitesutton, williamson, williamsonwohldmann, wilson, wilsonwashu, wing, wingxu, wohldmann, wohldmannwilson, xu, xuyu, yu, yuruben As you can see, GOPHER built on WAIS indices might fail to retrieve some authors heavily involved in publishing :-) More severely, retrieval expressions like 'mrna and mammalia' will give not the exprected results. Regards Reinhard -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-embldatabank@net.bio.net Sun Mar 12 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!news.alpha.net!solaris.cc.vt.edu!swiss.ans.net!paperboy.amoco.com!cronkite!usenet From: wmmounts@amoco.com (Bill Mounts) Newsgroups: bionet.molbio.embldatabank Subject: Re: SWISS-PROT File Formats... Date: 13 Mar 1995 14:25:32 GMT Organization: Amoco Corporation Lines: 29 Message-ID: <3k1kks$2ak@cronkite.amoco.com> References: <1995Mar12.222054.15798@nlm.nih.gov> Reply-To: wmmounts@amoco.com In article 15798@nlm.nih.gov, francis@borduas.nlm.nih.gov (Francis Ouellette) writes: > Bill Mounts (wmmounts@amoco.com) wrote: > > I am looking for definitions of the following of the following > > line codes which are currently in use with the SWISS-PROT > > database. Any help is greatly appreciated. > > > GN > > RP > > RC > > RM > > Bill, > > if you at the swiss-prot user manual you will find the > information below (and lots more too) > > regards, > > francis My primary reason for writing was because I didn't have the most recent set of docs. Thanks for your info, though. Bill From owner-embldatabank@net.bio.net Sun Mar 12 22:00:00 1995 Path: biosci!biosci!not-for-mail From: Bill Pearson Newsgroups: bionet.software,bionet.molbio.embldatabank,bionet.molbio.genbank,bionet.announce,bionet.molbio.proteins Subject: Re: FASTA 2.0x available Date: 13 Mar 1995 15:21:20 -0800 Organization: University of Virginia Lines: 30 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:11456 bionet.molbio.embldatabank:476 bionet.molbio.genbank:1976 bionet.announce:1891 bionet.molbio.proteins:3964 In article , Bill Pearson wrote: >A new (experimental) release of the FASTA program package is now >available from virginia.edu in pub/fasta/fasta20x.shar(.Z). Version >2.0x incorporates several major improvements in the FASTA and SSEARCH >(Smith-Waterman) sequence searching programs: >(2) FASTA now uses the rigorous Smith-Waterman algorithm to produce >alignments. Thus, there is no limit to gap size in alignments. ^^^ Several people have reported problems in compiling the programs due to oversights on my part. I believe that those problems have been fixed. Another person reported some problem downloading the programs. They are available via anonymous ftp from the machine "uvaarpa.virginia.edu", also known as "virginia.edu" and "128.143.2.7". FTP in as anonymous using your email address as the password. Keep those cards and letters coming. (If you have problems, an email message is more likely to get a prompt response than a newsgroup posting). Bill Pearson -- wrp@virginia.EDU Dept. of Biochemistry #440 U. of Virginia Charlottesville, VA 22908 From owner-embldatabank@net.bio.net Mon Mar 13 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.nysernet.net!news.sprintlink.net!uunet!fdn.fr!jussieu.fr!univ-lyon1.fr!serra.unipi.it!sirio.cineca.it!maya.dei.unipd.it!civ!stdvolp From: stdvolp@civ.bio.unipd.it (Studenti Volpin) Newsgroups: bionet.molbio.embldatabank Subject: 3D-reconstruction Date: 14 Mar 1995 16:01:39 GMT Organization: Biology Dept. - University of Padova - Italy Lines: 17 Distribution: eunet Message-ID: <3k4el3$7i6@maya.dei.unipd.it> NNTP-Posting-Host: civ.bio.unipd.it Hallo out there, I'm a PhD doing research on mouse development. I need a particular software which allow me to have a tridimensional picture of material under study starting from simple histological sections. I'm thinking about a scanning device with a reconstruction mathematical model. I have known that there are some people who are dealing with those kind of programs. Any suggestion? Please, e-mail addressing to stdvolp@cribi1.unipd.it Thank you in advance. Donatella From owner-embldatabank@net.bio.net Tue Mar 14 22:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!fdn.fr!uunet!news.tele.fi!news.funet.fi!news.cc.tut.fi!vuokko!bltihi From: bltihi@uta.fi (Timo Hiltunen) Newsgroups: bionet.molbio.genome-program,bionet.molbio.embldatabank,embnet.general Subject: Re: an EMBL gopher Followup-To: bionet.molbio.embldatabank Date: 14 Mar 1995 10:05:55 GMT Organization: University of Tampere, Finland Lines: 15 Distribution: world Message-ID: <3k3pq3$7fe@cc.tut.fi> References: <1995Mar12.085904.8295@comp.bioz.unibas.ch> NNTP-Posting-Host: vuokko.uta.fi X-Newsreader: TIN [version 1.2 PL1] Xref: biosci bionet.molbio.genome-program:1269 bionet.molbio.embldatabank:478 Reinhard Doelz (doelz@comp.bioz.unibas.ch) wrote: : To my knowledge, we run the only database gopher on EMBL and EMBL updates : world-wide. There are on average more than 300 requests served per day. : Peak requests are more than 1200 daily which is due to some unfortunate : ambition to run automaitc scripts. : Question for the community: How long will this service need to run? I, for example, use EMBL databank (in Switzerland) rather often, and think that there should be sequence databases that are also accessible via text-based (= non-WWW) methods. Timo Hiltunen from the Univ. of Tampere, Finland From owner-embldatabank@net.bio.net Wed Mar 15 22:00:00 1995 Newsgroups: bionet.software.srs,bionet.molbio.embldatabank Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: SRS-FTP gateway (beta release 1.1b) Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Thu, 16 Mar 1995 19:06:06 GMT Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 210 Xref: biosci bionet.software.srs:25 bionet.molbio.embldatabank:479 I sent this out a week ago, but due to local distribution problems, most of the world never saw it. For the people that did see the previous announcement, an important new feature is added, so do read on. Also people looking for non WWW access to the databases could be interested Included is a short manual on the use of an FTP to SRS gateway, developed in the EMBL Outstation - EBI. It can be used right now, but I do not garantee yet, that the service will be officially supported. Please try it, and if you find any problems, or have any suggestions, let me know (jecop@ebi.ac.uk) The idea is that it can be used in automated checking/retrieving new sequences of interest. Jeroen - USING SRS (Sequence Retrieval System [1]) from Anonymous FTP ------------------------------------------------------------ (Jeroen Coppieters, 17-Mar-1995, srsftp version 1.1beta) This document describes SRSFTP as it is maintained at EMBL Outstation, the European Bioinformatics Institute further referenced as "the EBI" The Anonymous FTP server of the EBI has a gateway to SRS, developped by Jeroen Coppieters and RJ White. This allows the retrieval of sequences from Swissprot and EMBL (as well as all other databases that are maintained in SRS at the EBI [2]), using the power of SRS. A query can be executed from any directory, after connecting to the anonymous ftp server. All results of the query will be stored in the file you name. The sequences are stored in flat-file EMBL format by default In any query, the * wildcard can be used three formats of queries are available: - simple sequence retrieval - simple srs query - full srs query 1) SIMPLE SEQUENCE RETRIEVAL --------------------------- FORMAT: get DB:INDEX:QUERYSTRING FILENAME DB is one of the following: embl, emblnew, emblall, nuc swissprot, swissnew, swissall, pep if any of the xxall databases is specified, both the release and the updates are searched. If a sequence has been updated since the last release, both the old and new entry will be returned. INDEX DATABASE SEARCHFIELD QUERYSTRING acc accession number accession nr (e.g. X07888) id identifier identifier (e.g. ATP6_YEAST) dat date date (e.g. 20-NOV-1994) fts feature feature name (e.g. intron) ref reference Journal reference (e.g. Plant Mol. Biol. 10:91-104(1987)) sl sequence length number (e.g. 2400) or range (e.g. 2300:5000) def definition string aut author string cc comment string org organism string tit reference title string all all text fields string EXAMPLES: get emblall:acc:x07888 x07888.seq retrieve sequence from embl/emnew with accession number x07888 store in the file x07888.seq get swissprot:all:nitrate* nitrate.pep get all swissprot entries that have a word starting with nitrate in any of the text fields. Store in the file nitrate.pep 2) SIMPLE SRS QUERY ------------------ FORMAT: get srs:QUERYSTRING This allows linking of several databases For more information on SRS queries, have a look at the SRS manual This however does not allow the complete functionality of SRS. Restrictions are: - NO SPACES are allowed in the query. - no command line parameters can be included EXAMPLES get srs:[embl-fts:intron]>parent&[embl-org:arabidopsis*] arain.seq retrieve all sequences from Arabidopsis spec. that contain an intron. get srs:[prosite-id:PROTEIN_KINASE_TYR]>swissprot kinase.pep retrieve all proteins, that contain a tyrosine kinase motif (PROSITE) get srs:[prosite-id:PROTEIN_KINASE_TYR]>swissprot>pdb kinase.pdb retrieve 3D structures (if known) from the above proteins 3) FULL SRS QUERY ----------------- If you want to have access to command line options (e.g. to change the output format), a full blown getz command is available. FORMAT: From UNIX, VMS+Multinet, MSDOS+NCSA ftp: get getz+commandline+options+querystring filename VMS+UCX: get "getz+commandline+options+querystring" filename - All spaces in the query should be replaced by plus (+) - If you want to include a + in a query, use a double plus (++) - do not put quotes round the querystring - if you want to escape a character with a backslash (\), duplicate the backslash (\\) - contrary to forms 1 and 2, there is no colon in the command - the getz program has a new command line option -pipe "string" where string can be "/bin/compress" or "/bin/gzip" this will compress the results before transmitting the data, thus minimizing network traffic Do not forget to use BINARY TRANSFER if you use this option - On UNIX systems, whenever ftp expects a filename, this can be replaced by - (dash) the retrieved file will be printed on stdout EXAMPLES get getz+-help file retrieve help on the usage of getz get getz+-libs libs.lst get a list of all available databases get getz+-d+-sf+fasta+-pipe+"/bin/gzip"+[emnew-org:drosophila*] dro.seq.gz retrieve all Drosophila sp. sequences from emnew in fasta format. Gzip before transmitting get getz+-l+swissprot+-l+swissnew+[sq-id:*_ecoli] ecoli.lst generate a list of all ecoli proteins in swissprot and swissnew ============================================================ NOTES: ----- [1] More information on SRS is available from the author: Thure Etzold Via WWW: http://www.embl-heidelberg.de/srs/srsman.html Refererences: Thure Etzold and Patrick Argos, SRS an indexing and retrieval tool for flat file data libraries. Comput. Appl. Biosci. 9:49-57, 1993 Thure Etzold and Patrick Argos, Transforming a set of biological flat file libraries to a fast access network. Appl. Biosci. 9:59-64, 1993 [2] on March 14th 1995, these database were: Library Group Entries Index Date ------------------------------------------------------------------- SWISSPROT Sequence 40292 2/28/95 SWISSNEW Sequence 9036 3/8/95 PIR Sequence 71995 2/28/95 EMBL Sequence 234501 2/28/95 EMNEW Sequence 102576 3/14/95 NRL3D Sequence 4153 3/1/95 NRSUB Sequence 248 3/1/95 PDB ProteinStruct 3391 3/1/95 HSSP ProteinStruct 3070 3/4/95 DSSP ProteinStruct 2968 3/2/95 ALI ProteinStruct 84 3/1/95 FSSP ProteinStruct 436 3/4/95 PROSITE SeqRelated 1029 3/1/95 PROSITEDOC SeqRelated 786 3/1/95 BLOCKS SeqRelated 770 3/1/95 EPD SeqRelated 1251 3/1/95 ECDC SeqRelated 3571 3/1/95 ENZYME SeqRelated 3546 3/1/95 REBASE SeqRelated 2454 3/1/95 PRODOM SeqRelated 23105 3/1/95 FLYGENE SeqRelated 7126 3/10/95 SWISSDOM SeqRelated 28224 3/1/95 PIRALN SeqRelated 1183 3/1/95 SEQANALREF Literature 2579 3/1/95 MEDLINE Literature 179262 3/1/95 LIMB Others 120 3/1/95 TFSITE TransFac 4042 3/14/95 TFFACTOR TransFac 1412 3/14/95 DBEST TaggedSites 3264 3/8/95 -- ====================================================================== . O . Jeroen Coppieters . O O o O . Software Support O O O O *o O O Jeroen.Coppieters@embl-ebi.ac.uk O O O O( *o )O O (or jecop@ebi.ac.uk) )O O O O o* O O( ++44 1223 494422 O O O O( o* )O O )O O O O *o O O( EMBL Outstation EBI O O O O( *o )O O (European Bioinformatics Institute) )O @ O O o* O O( Hinxton Hall O O O( o* )O(' Hinxton ` O( *o O ' Cambridge CB10 1RQ ` O ' UK http://www.ebi.ac.uk ====================================================================== From owner-embldatabank@net.bio.net Thu Mar 16 22:00:00 1995 Newsgroups: bionet.molbio.embldatabank Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: Re: an EMBL gopher Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Thu, 16 Mar 1995 19:17:37 GMT References: <1995Mar12.085904.8295@comp.bioz.unibas.ch> <3k3pq3$7fe@cc.tut.fi> Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 50 Timo Hiltunen (bltihi@uta.fi) wrote: : Reinhard Doelz (doelz@comp.bioz.unibas.ch) wrote: : : To my knowledge, we run the only database gopher on EMBL and EMBL updates : : world-wide. There are on average more than 300 requests served per day. : : Peak requests are more than 1200 daily which is due to some unfortunate : : ambition to run automaitc scripts. : : Question for the community: How long will this service need to run? : I, for example, use EMBL databank (in Switzerland) rather often, and think : that there should be sequence databases that are also accessible via : text-based (= non-WWW) methods. In another post I just announced an ftp based access method. Would a similar gopher system be of more use? I could develop a similar gateway from gopher to SRS At the moment I've set up a simple one (only allowing retrieval by accesion number or entry name) as a quick test. Have a look on gopher.ebi.ac.uk --> 9. (Experimental) Sequence retrieval from EMBL/SWISSPROT database/ --> 1. Sequence retrieval from Swissprot 2. Sequence retrieval from EMBL But, please, do not hardcode this. As said, it's just a quick test, so - it can still go wrong - it could have to move somewheree else in the gopher-tree - I have no authorization from EMBL/EBI to support this as an official service Let's here some comments : Timo Hiltunen : from the Univ. of Tampere, Finland Jeroen Coppieters -- ====================================================================== . O . Jeroen Coppieters . O O o O . Software Support O O O O *o O O Jeroen.Coppieters@embl-ebi.ac.uk O O O O( *o )O O (or jecop@ebi.ac.uk) )O O O O o* O O( ++44 1223 494422 O O O O( o* )O O )O O O O *o O O( EMBL Outstation EBI O O O O( *o )O O (European Bioinformatics Institute) )O @ O O o* O O( Hinxton Hall O O O( o* )O(' Hinxton ` O( *o O ' Cambridge CB10 1RQ ` O ' UK http://www.ebi.ac.uk ====================================================================== From owner-embldatabank@net.bio.net Thu Mar 16 22:00:00 1995 Newsgroups: bionet.molbio.embldatabank Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@embl-ebi.ac.uk (Jeroen Coppieters) Subject: Re: an EMBL gopher Message-ID: Sender: jecop@ebi.ac.uk (Jeroen Coppieters) Date: Fri, 17 Mar 1995 09:37:46 GMT Lines: 52 Reply-To: jecop@embl-ebi.ac.uk (Jeroen Coppieters) Organization: EMBL Outstation - EBI, Hinxton Hall, UK X-Newsreader: mxrn 6.18-16 Followup-To: bionet.molbio.embldatabank Timo Hiltunen (bltihi@uta.fi) wrote: : Reinhard Doelz (doelz@comp.bioz.unibas.ch) wrote: : : To my knowledge, we run the only database gopher on EMBL and EMBL updates : : world-wide. There are on average more than 300 requests served per day. : : Peak requests are more than 1200 daily which is due to some unfortunate : : ambition to run automaitc scripts. : : Question for the community: How long will this service need to run? : I, for example, use EMBL databank (in Switzerland) rather often, and think : that there should be sequence databases that are also accessible via : text-based (= non-WWW) methods. In another post I just announced an ftp based access method. Would a similar gopher system be of more use? I could develop a similar gateway from gopher to SRS At the moment I've set up a simple one (only allowing retrieval by accesion number or entry name) as a quick test. Have a look on gopher.ebi.ac.uk --> 9. (Experimental) Sequence retrieval from EMBL/SWISSPROT database/ --> 1. Sequence retrieval from Swissprot 2. Sequence retrieval from EMBL But, please, do not hardcode this. As said, it's just a quick test, so - it can still go wrong - it could have to move somewheree else in the gopher-tree - I have no authorization from EMBL/EBI to support this as an official service Let's here some comments : Timo Hiltunen : from the Univ. of Tampere, Finland Jeroen Coppieters -- ====================================================================== . O . Jeroen Coppieters . O O o O . Software Support O O O O *o O O Jeroen.Coppieters@embl-ebi.ac.uk O O O O( *o )O O (or jecop@ebi.ac.uk) )O O O O o* O O( ++44 1223 494422 O O O O( o* )O O )O O O O *o O O( EMBL Outstation EBI O O O O( *o )O O (European Bioinformatics Institute) )O @ O O o* O O( Hinxton Hall O O O( o* )O(' Hinxton ` O( *o O ' Cambridge CB10 1RQ ` O ' UK http://www.ebi.ac.uk ====================================================================== From owner-embldatabank@net.bio.net Tue Mar 21 22:00:00 1995 Newsgroups: bionet.molbio.embldatabank,ebi.general,embnet.general Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!stoehr From: stoehr@ebi.ac.uk (Peter Stoehr) Subject: EMBL Release 42 built Sender: news@ebi.ac.uk (Mr news) Message-ID: <1995Mar22.123438@ebi.ac.uk> Date: Wed, 22 Mar 1995 11:34:38 GMT Lines: 96 Organization: European BioInformatics Institute Release 42 of the EMBL Nucleotide Sequence Database (March 1995) is built and installed on the EBI's e-mail, anonymous FTP, FASTA and WWW servers. It is also installed already at some EMBnet sites. Some extracts from the release notes are appended below. Regards, Peter Stoehr EMBL - EBI ----------- 1 RELEASE 42 The EMBL nucleotide sequence database was frozen to make Release 42 on 8th March 1995. The release contains 303206 sequence entries comprising 262,559,786 nucleotides. This represents an increase of about 16% over Release 41. A breakdown of Release 42 by taxonomic division is shown below: Division Entries Nucleotides ----------------- ------- ------------ Bacteriophage 1066 1493417 ESTs 123526 39332522 Fungi 8420 19940449 Invertebrates 13831 27610495 Organelles 8195 9364254 Other Mammals 6272 6976315 Other Vertebrates 7041 8144622 Plants 11105 14145431 Primates 35290 36665648 Prokaryotes 21427 37074154 Rodents 23626 26850022 STSs 7232 2288477 Synthetic 8597 4295284 Unclassified 6082 3577630 Viruses 21496 24801066 ----------------- ------- ------------ Total 303206 262559786 plus: Other patents 6686 2507063 ----------------- ------- ------------ Grand Total 309892 265066849 1.1 Literature Reference Identifiers As previously announced, we have introduced at this release identifiers into journal references. We have created a new RX line-type, which will be optional for any reference in the database, with the following format: RX database_name; identifier. e.g. RN [1] RP 1-549 RX MEDLINE; 82196900. RA Hennighausen L.G., Sippel A.E.; RT "Mouse whey acidic protein is a novel member of the family of RT 'four-disulfide core' proteins"; RL Nucleic Acids Res. 10:2677-2684(1982). In this release, there are links to over 50,000 MEDLINE records. 2 FORTHCOMING CHANGES 2.1 Accession Numbers It will soon be necessary to extend the range of possible accession numbers available for the nucleotide sequence databases. This will be an important topic for an upcoming collaborative meeting between EMBL, GenBank and DDBJ, and we do not wish to preempt the result of that discussion. Inevitably though, there must be a change to the present structure of accession numbers which consist of one prefix letter followed by 5 digits (eg X12399), and it is very likely that accession numbers will become longer and contain more prefix letters. Existing accession numbers will remain valid as is. We will announce such a significant change as widely, and with as much advance notice, as possible. 2.2 EST Database Divisions The number of EST sequences is growing rapidly and will continue to do so for some time. In order to keep the size of the data files within reasonable limits for handling purposes, we propose to split the EST division into several files named EST1.DAT, EST2.DAT etc at the next release (Release 43, June 1995). 2.3 Feature Identifiers We are investigating ways of assigning unique identifiers to sequence features described within the Feature Table. We will initially focus on CDS features to enable a finer level of cross-referencing than at present between the nucleotide and protein sequence databases. We are hoping to adopt a common approach with our collaborators at DDBJ and GenBank. From owner-embldatabank@net.bio.net Fri Mar 24 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.molbio.embldatabank Subject: help Date: 25 Mar 1995 03:19:09 -0000 Lines: 1 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3l023d$r4m@mserv1.dl.ac.uk> Original-To: embl-db@vikram!dl.ac.uk.ncst.ernet.in From owner-embldatabank@net.bio.net Tue Mar 28 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nntp.uio.no!usenet From: yihena@ifi.uio.no(YichengAn) Newsgroups: bionet.molbio.embldatabank Subject: What'd you expect ? Date: 29 Mar 1995 09:38:41 GMT Organization: University of Oslo Lines: 28 Message-ID: <3lb9r1$180@hermod.uio.no> Reply-To: yichena@ifi.uio.no NNTP-Posting-Host: biotek08.uio.no X-Newsreader: WinVN 0.92.3 Hi, I 've started to work on a DNA sequence analysis software tools, without being asked by anybody, basically. So here I am to collect your suggestions, which can be anything, from output formats to functionality. It's going to be work on-linely through WWW, and to be sort of free-access-ware, so what you'll suggest is probably what you'll get. Another thing is I need your explanation of what it means by DNA sequencial repeatings, (it's a shame because I'm myself a Master program student in protein studies). If you got a sequence as follows: ????ATTGCG??????GTTGCA??????ATTGCG????? so the longer repeatings are: |<---------->| |<---------->| ????ATTGCG??????GTTGCA??????ATTGCG????? but then, would you expect to see the shorter redundant one like: |<------>| |<----->| |<------>| ????ATTGCG??????GTTGCA??????ATTGCG????? Contact me, Thanks! Regards, Yicheng From owner-embldatabank@net.bio.net Fri Mar 31 23:00:00 1995 Path: biosci!mahidol.ac.th!gsctlr From: gsctlr@mahidol.ac.th (Thianchai Lakornrach - SCBT - 3636209) Newsgroups: bionet.molbio.embldatabank Subject: artificial lipase sequence Date: 1 Apr 1995 06:57:46 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net 1 I would like to know the meaning of an artificial gene. Where is it derive from such as artifitial gene for lipase ? 2 How to get the details of these following sequences? embl A 02815 embl A 02816 U 17036 NCBI gi:608524, 608525, 608526 Thank you for your help. THIANCHAI LAKORNRACH MAHIDOL UNIVERSITY BANGKOK THAILAND