From owner-bionews@hgmp.mrc.ac.uk Mon Dec 17 18:47:02 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 0250117B07 for ; Mon, 17 Dec 2001 18:46:59 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 80F9917B02 for ; Mon, 17 Dec 2001 18:46:57 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6022) id A233217AFF; Mon, 17 Dec 2001 18:46:56 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 6C92B17AF8 for ; Mon, 17 Dec 2001 11:03:14 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id DD06717A69 for ; Mon, 17 Dec 2001 11:03:12 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA07971 for bionet-announce@net.bio.net; Mon, 17 Dec 2001 11:03:12 GMT To: bionet-announce@net.bio.net From: Maria Jesus Martin Newsgroups: bionet.announce Subject: Release 19 of TREMBL, a protein sequence database supplementing SWISS-PROT Organization: EMBL-EBI Message-ID: <3C1DD0F0.E6B9A335@ebi.ac.uk> Reply-To: martin@ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 1008586992 7746 193.62.199.192 (17 Dec 2001 11:03:12 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: Mon, 17 Dec 2001 11:03:12 +0000 (UTC) X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.2.17-14 i686) X-Accept-Language: en Date: Mon, 17 Dec 2001 18:46:56 +0000 (GMT) Sender: owner-bionews@hgmp.mrc.ac.uk Precedence: bulk INTRODUCTION ============ TrEMBL is a computer-annotated protein sequence database supplementing the SWISS-PROT Protein Knowledgebase. TrEMBL contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database not yet integrated in SWISS-PROT. TrEMBL can be considered as a preliminary section of SWISS-PROT. For all TrEMBL entries which should finally be upgraded to the standard SWISS-PROT quality, SWISS-PROT accession numbers have been assigned. RELEASE 19.0 OF TrEMBL ===================== This TrEMBL release was created from the EMBL Nucleotide Sequence Database release 68 and updates until 16.11.01 and contains 636'825 entries and 184'332'036 amino acids. To minimize redundancy, the translations of all coding sequences (CDS) in the EMBL Nucleotide Sequence Database already included in SWISS-PROT release 40 and updates until 13.12.01 have been removed from TrEMBL release 19. TrEMBL is split in two main sections: SP-TrEMBL and REM-TrEMBL: SP-TrEMBL (SWISS-PROT TrEMBL) contains the entries (562'222) which should be eventually incorporated into SWISS-PROT. SWISS-PROT accession numbers have been assigned for all SP-TrEMBL entries. SP-TrEMBL is organized in subsections: arc.dat (Archaea): 1692 entries arp.dat (Complete Archaeal proteomes):19590 entries fun.dat (Fungi): 13339 entries hum.dat (Human): 29064 entries inv.dat (Invertebrates): 60611 entries mam.dat (Other Mammals): 9724 entries mhc.dat (MHC proteins): 7434 entries org.dat (Organelles): 50792 entries phg.dat (Bacteriophages): 4368 entries pln.dat (Plants): 58841 entries pro.dat (Prokaryotes): 69426 entries prp.dat (Complete Prokaryote Proteomes):74477 entries rod.dat (Rodents): 24185 entries unc.dat (Unclassified): 252 entries vrl.dat (Viruses): 60309 entries vrt.dat (Other Vertebrates): 11003 entries vrv.dat (Retroviruses): 67115 entries 80'772 new entries have been integrated in SP-TrEMBL. The sequences of 1388 SP-TrEMBL entries have been updated and the annotation has been updated in 321'110 entries. In the document deleteac.txt, you will find a list of all accession numbers which were previously present in TrEMBL, but which have now been deleted from the database. REM-TrEMBL (REMaining TrEMBL) contains the entries (74'603) that we do not want to include in SWISS-PROT. ACCESS/DATA DISTRIBUTION ======================== FTP server: ftp.ebi.ac.uk/pub/databases/trembl SRS server: http://srs.ebi.ac.uk/ TrEMBL is also available on the SWISS-PROT CD-ROM. SWISS-PROT + TrEMBL is searchable on the following servers at the EBI: FASTA3 (http://www.ebi.ac.uk/fasta33/) BLAST2 (http://www.ebi.ac.uk/blast2/) Bic_sw (http://www.ebi.ac.uk/bic_sw/) Scanps (http://www.ebi.ac.uk/scanps/) MPSrch (http://www.ebi.ac.uk/MPsrch/) TrEMBL HAS BEEN PREPARED BY: ============================ Rolf Apweiler, Kirsty Bates, Margaret Biswas, Sergio Contrino, Daniel Barrell, Kirill Degtyarenko, Wolfgang Fleischmann, Gill Fraser, Henning Hermjakob, Kati Laiho, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Minna Lehvaslaiho, Michele Magrane, Maria Jesus Martin, Virginie Mittard, Nicola Mulder, Claire O'Donovan, John F. O'Rourke, Eleanor Whitfield and Allyson Williams at the EMBL Outstation - European Bioinformatics Institute (EBI) in Hinxton, UK; Amos Bairoch, Isabelle Phan, Sandrine Pilbout and Alain Gateau at the Swiss Institute of Bioinformatics in Geneva, Switzerland. ------------------------------------------ Maria Jesus Martin email:martin@ebi.ac.uk EMBL Outstation EBI (European Bioinformatics Institute) URL: http://www.ebi.ac.uk Wellcome Trust Genome Campus Tel: +44 (1223) 494408 Hinxton fax: +44 (1223) 494468 Cambridge CB10 1SD UK ---------------------------------------- .