From owner-bionews@hgmp.mrc.ac.uk Mon Jun 24 10:56:04 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 90CB817B7D for ; Mon, 24 Jun 2002 10:55:50 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B294017B5C for ; Mon, 24 Jun 2002 10:55:38 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6022) id 5B43117B38; Mon, 24 Jun 2002 10:52:43 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 86BC217C07 for ; Mon, 24 Jun 2002 10:08:54 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2DE3417C30 for ; Mon, 24 Jun 2002 09:57:41 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA09168 for bionet-announce@net.bio.net; Mon, 24 Jun 2002 09:57:41 +0100 (BST) To: bionet-announce@net.bio.net From: Maria Jesus Martin Newsgroups: bionet.announce Subject: Release 21 of TREMBL, a protein sequence database supplementing SWISS-PROT Organization: EMBL-EBI Message-ID: <3D16DF05.76CD2C2F@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 1024909061 8937 193.62.199.192 (24 Jun 2002 08:57:41 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: Mon, 24 Jun 2002 08:57:41 +0000 (UTC) X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.2.17-14 i686) X-Accept-Language: en Date: Mon, 24 Jun 2002 10:52:43 +0100 (BST) 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/GenBank/DDBJ Nucleotide Sequence Databases and also protein sequences extracted from the literature or submitted to SWISS-PROT, which are not yet integrated into 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 21.0 OF TrEMBL ===================== This TrEMBL release was created from the EMBL Nucleotide Sequence Database release 70 and updates until 07.05.02 and contains 751'148 entries and 218'504'701 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 21.06.02 have been removed from TrEMBL release 21. TrEMBL is split in two main sections: SP-TrEMBL and REM-TrEMBL: SP-TrEMBL (SWISS-PROT TrEMBL) contains the entries (671'580) 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): 1644 entries arp.dat (Complete Archaeal proteomes): 29757 entries fun.dat (Fungi): 14606 entries hum.dat (Human): 29766 entries inv.dat (Invertebrates): 68301 entries mam.dat (Other Mammals): 10511 entries mhc.dat (MHC proteins): 8069 entries org.dat (Organelles): 58906 entries phg.dat (Bacteriophages): 5676 entries pln.dat (Plants): 67339 entries pro.dat (Prokaryotes): 66680 entries prp.dat (Complete Prokaryotic Proteomes):123685 entries rod.dat (Rodents): 27467 entries unc.dat (Unclassified): 143 entries vrl.dat (Viruses): 71522 entries vrt.dat (Other Vertebrates): 12279 entries vrv.dat (Retroviruses): 75229 entries 56'042 new entries have been integrated in SP-TrEMBL. The sequences of 810 SP-TrEMBL entries have been updated and the annotation has been updated in 189'983 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 (79'568) 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/) For each TrEMBL release, a synchronized version of the concurrent SWISS-PROT release is distributed at ftp.ebi.ac.uk/pub/databases/trembl/swissprot/ We also produce every week a complete non-redundant protein sequence collection by providing three compressed files (these are in the directory /pub/databases/sp_tr_nrdb on the EBI FTP server and in databases/sp_tr_nrdb on the ExPASy server): sprot.dat.gz, trembl.dat.gz and trembl_new.dat.gz. TrEMBL HAS BEEN PREPARED BY: ============================ Maria Jesus Martin, Claire O'Donovan, Allyson Williams, Daniel Barrell, Philippe Aldebert, Rolf Apweiler, Kirsty Bates, Paul Browne, Sergio Contrino, Kirill Degtyarenko, Gill Fraser, Henning Hermjakob, Kati Laiho, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Minna Lehvaslaiho, Michele Magrane, Virginie Mittard, Nicola Mulder, John F. O'Rourke, Sandra Orchard, Sandra van den Broek, Eleanor Whitfield and at the EMBL Outstation - European Bioinformatics Institute (EBI) in Hinxton, UK; Amos Bairoch, Alain Gateau, Alexandre Gattiker, Isabelle Phan and Sandrine Pilbout 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 -------------------------------------------- .