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UniProtKB/TrEMBL - Old Release Notes

N.B. From release 27, the UniProtKB/TrEMBL release notes are included in the UniProt release notes.

		TrEMBL Release Notes 
Release 6, June 1998
EMBL Outstation European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Telephone: (+44 1223) 494 400 Fax: (+44 1223) 494 468 Electronic mail address: DATALIB@EBI.AC.UK WWW server: http://www.ebi.ac.uk/ Amos Bairoch Medical Biochemistry Department Centre Medical Universitaire 1211 Geneva 4 Switzerland Telephone: (+41 22) 784 40 82 Fax: (+41 22) 702 55 02 Electronic mail address: BAIROCH@CMU.UNIGE.CH WWW server: http://www.expasy.ch/ INTRODUCTION ============ TREMBL is a protein sequence database supplementing the Swiss-Prot Protein Sequence Data Bank. 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 6.0 OF TREMBL ===================== This TREMBL release is created from the EMBL Nucleotide Sequence Database release 54 and contains 177'757 sequence entries, comprising 48'796'878 amino acids. TREMBL is split in two main sections; SP-TREMBL and REM-TREMBL: SP-TREMBL (Swiss-Prot TREMBL) contains the entries (150'329) which should be eventually incorporated into Swiss-Prot. Swiss-Prot accession numbers have been assigned for all SP-TREMBL entries. SP-TREMBL is organised in subsections: arc.dat (Archea): 5556 entries (new section) fun.dat (Fungi): 4781 entries hum.dat (Human): 6312 entries inv.dat (Invertebrates): 20364 entries mam.dat (Other Mammals): 2450 entries mhc.dat (MHC proteins): 3524 entries org.dat (Organelles): 11685 entries phg.dat (Bacteriophages): 1240 entries pln.dat (Plants): 11217 entries pro.dat (Prokaryotes): 32000 entries rod.dat (Rodents): 5913 entries unc.dat (Unclassified): 88 entries vrl.dat (Viruses): 41882 entries vrt.dat (Other Vertebrates): 3317 entries REM-TREMBL (REMaining TREMBL) contains the entries (27'428) that we do not want to include in Swiss-Prot. REM-TrEMBL entries have no accession numbers. This section is organised in five subsections: 1) Immunoglobulins and T-cell receptors (Immuno.dat) Most REM-TrEMBL entries are immunoglobulins and T-cell receptors. We stopped entering immunoglobulins and T-cell receptors into Swiss-Prot, because we only want to keep the germ line gene derived translations of these proteins in Swiss-Prot and not all known somatic recombinated variations of these proteins. We would like to create a specialised database dealing with these sequences as a further supplement to Swiss-Prot and keep only a representative cross-section of these proteins in Swiss-Prot. 2) Synthetic sequences (Synth.dat) Another category of data, which will not be included in Swiss-Prot are synthetic sequences. Again, we do not want to leave these entries in TrEMBL. Ideally one should build a specialised database for artificial sequences as a further supplement to Swiss-Prot. 3) Patent application sequences (Patent.dat) A third subsection consists of coding sequences captured from patent applications. A thorough survey of these entries have shown that apart from a rather small minority (which in most cases have already been integrated in Swiss-Prot), most of these sequences contain either erroneous data or concern artificially generated sequences outside the scope of Swiss-Prot. 4) Small fragments (Smalls.dat) Another subsection consists of fragments with less than eight amino acids. 5) CDS not coding for real proteins (Pseudo.dat) The last subsection consists of CDS translations where we have strong evidence to believe that these CDS are not coding for real proteins. WEEKLY UPDATES OF TREMBL AND NON-REDUNDANT DATA SETS ==================================================== Weekly cumulative updates of TREMBL are available by anonymous FTP and from the EBI SRS server. 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): sprot.dat.Z, trembl.dat.Z and trembl_new.dat.Z. ACCESS/DATA DISTRIBUTION ======================== FTP server: ftp.ebi.ac.uk/pub/databases/trembl SRS server: http://srs.ebi.ac.uk:5000/ TREMBL is also available on the Swiss-Prot CD-ROM. Swiss-Prot + TREMBL is searchable on the FASTA3, BLAST2 and Bic_sw servers of the EBI. TREMBL HAS BEEN PREPARED BY: ============================ Rolf Apweiler, Christian Desaintes, Sergio Contrino, Wolfgang Fleischmann, Henning Hermjakob, Vivien Junker, Stephanie Kappus, Fiona Lang, Michele Magrane, Maria Jesus Martin, Steffen Moeller, Nicoletta Mitaritonna and Claire O'Donovan at the EMBL Outstation - European Bioinformatics Institute (EBI) in Hinxton, UK; Amos Bairoch and Alain Gateau at the Medical Biochemistry Department of the University of Geneva, Switzerland. Notes ===== This manual and the database it accompanies may be copied and redistributed freely, without advance permission, provided that this statement is reproduced with each copy. Citation ======== If you want to cite TREMBL in a publication please use the following reference: Bairoch A., and Apweiler R. The Swiss-Prot protein sequence data bank and its supplement TREMBL in 1998. Nucleic Acids Res. 26:38-42(1998).


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