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 19, December 2001 EMBL Outstation European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Telephone: (+44 1223) 494 444 Fax: (+44 1223) 494 468 Electronic mail address: DATALIB@EBI.AC.UK WWW server: http://www.ebi.ac.uk/ Swiss Institute of Bioinformatics (SIB) Centre Medical Universitaire 1, rue Michel Servet 1211 Geneva 4 Switzerland Telephone: (+41 22) 702 50 50 Fax: (+41 22) 702 58 58 Electronic mail address: Amos.Bairoch@isb-sib.ch WWW server: http://www.expasy.org/ Acknowledgements TrEMBL has been prepared by: o 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; o Amos Bairoch, Alain Gateau, Isabelle Phan and Sandrine Pilbout at the Swiss Institute of Bioinformatics in Geneva, Switzerland. Copyright Notice TrEMBL copyright (c) 2000 EMBL-EBI This manual and the database it accompanies may be copied and redistributed freely, without advance permission, provided that this copyright 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 2000. Nucl. Acids Res. 28:45-48(2000). 1. 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. 2. Why a supplement to Swiss-Prot? The ongoing gene sequencing and mapping projects have dramatically increased the number of protein sequences to be incorporated into Swiss-Prot. We do not want to dilute the quality standards of Swiss-Prot by incorporating sequences without proper sequence analysis and annotation, but we do want to make the sequences available as fast as possible. TrEMBL achieves this second goal, and is a major step in the process of speeding up subsequent upgrading of annotation to the standard Swiss-Prot quality. To address the problem of redundancy, the translations of all coding sequences (CDS) in the EMBL Nucleotide Sequence Database already included in Swiss-Prot have been removed from TrEMBL. 3. The Release 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 minimise 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 organised 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. REM-TrEMBL entries have no accession numbers. This section is organised in six 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) This subsection consists of CDS translations where we have strong evidence to believe that these CDS are not coding for real proteins. 6) Truncated proteins (Truncated.dat) The last subsection consists of truncated proteins which result from events like mutations introducing a stop codon leading to the truncation of the protein product. 4. Format Differences Between Swiss-Prot and TrEMBL The format and conventions used by TrEMBL follow as closely as possible that of Swiss-Prot. Hence, it is not necessary to produce an additional user manual and extensive release notes for TrEMBL. The information given in the Swiss-Prot release notes and user manual are in general valid for TrEMBL. The differences are mentioned below. The general structure of an entry is identical in Swiss-Prot and TrEMBL. The data class used in TrEMBL (in the ID line) is always 'PRELIMINARY', whereas in Swiss-Prot it is always 'STANDARD'. Differences in line types present in Swiss-Prot and TrEMBL: The ID line (IDentification): The entry name used in SP-TrEMBL is the same as the Accession Number of the entry. The entry name used in REM-TrEMBL is the stable part of the protein_id tagged to the corresponding CDS in the EMBL Nucleotide Sequence Database. 'protein_id' stands for the "Protein Identification" number. It is a number that you will find in the feature table of the EMBL nucleotide sequence entries in a qualifier called "/protein_id" which is tagged to every CDS. Example: FT CDS 339..1514 FT /codon_start=1 FT /db_xref="PID:g1256015" FT /product="dystrobrevin-epsilon" FT /protein_id="AAC50431.1" The protein_id is defined as follows in the The DDBJ/EMBL/GenBank Feature Table Definition documentation Qualifier /protein_id Definition Protein Identifier, issued by International collaborators. This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. Value format