TrEMBL release 4.0
Published July 1, 1997
TREMBL Release Notes Release 4, Jul 1997 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://expasy.hcuge.ch/ Acknowledgements TREMBL has been prepared by: o Rolf Apweiler, Sergio Contrino, Vivien Junker, Stephanie Kappus, Fiona Lang, Michele Magrane, Maria Jesus Martin, Nicoletta Mitaritonna and Claire O'Donovan at the EMBL Outstation - European Bioinformatics Institute (EBI) in Hinxton, UK; o 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. Nucleic Acids Res. 25:31-26(1997). 1. Introduction TREMBL is a computer-annotated 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. 2. Why a supplement to SWISS-PROT? The ongoing genome 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. We name this supplement TREMBL (TRanslation from EMBL), since the tools used to create the translations of the CDS are based on the program 'trembl' written by Thure Etzold at the EMBL. 3. The Release This TREMBL release is created from the EMBL Nucleotide Sequence Database release 51 and contains 139'208 sequence entries, comprising 37'836'288 amino acids. To minimize redundancy, the translations of all coding sequences (CDS) in the EMBL Nucleotide Sequence Database already included in SWISS-PROT Release 34 and in SWISS-PROT updates by 21.7. have been removed from TREMBL release 4. TREMBL is split in two main sections; SP-TREMBL and REM-TREMBL: SP-TREMBL (SWISS-PROT TREMBL) contains the entries (116'769) 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: fun.dat (Fungi): 3757 entries hum.dat (Human): 5605 entries inv.dat (Invertebrates): 15940 entries mam.dat (Other Mammals): 2081 entries mhc.dat (MHC proteins): 2694 entries org.dat (Organelles): 8213 entries phg.dat (Bacteriophages): 961 entries pln.dat (Plants): 7776 entries pro.dat (Prokaryotes): 26576 entries rod.dat (Rodents): 5551 entries unc.dat (Unclassified): 279 entries vrl.dat (Viruses): 34508 entries vrt.dat (Other Vertebrates): 2828 entries REM-TREMBL (REMaining TREMBL) contains the entries (22'439) that we do not want to include in SWISS-PROT.REM-TREMBL entries have no accession numbers. This section is organized in five subsections: 1) Immunoglobulins and T-cell receptors Most REM-TREMBL entries will be 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 specialized 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 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 specialized database for artificial sequences as a further supplement to SWISS-PROT. 3) Patent application sequences 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 contains either erroneous data or concern artificially generated sequences outside the scope of SWISS-PROT. 4) Small fragments Another subsection consists of fragments with less than seven amino acids. 5) CDS not coding for real proteins The last subsection consists of CDS translations where we have strong evidence to believe that these CDS are not coding for real proteins. 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 PID tagged to the corresponding CDS in the EMBL Nucleotide Sequence Database. 'PID' stands for the "Protein IDentification" number. It is a number that you will find in EMBL nucleotide sequence entries in a qualifier called "/db_xref" which is tagged to every CDS in the nucleotide database. Example: FT CDS 54..1382 FT /note="ribulose-1,5-bisphosphate carboxylase/ FT oxygenase activase precursor" FT /db_xref="PID:g1006835" The DT line (DaTe) The format of the DT lines that serve to indicate when an entry was created and updated are identical to that defined in SWISS-PROT; but the DT lines in TREMBL are referring to the TREMBL release. The difference is shown in the example below. DT lines in a SWISS-PROT entry: DT 01-JAN-1988 (REL. 06, CREATED) DT 01-JUL-1989 (REL. 11, LAST SEQUENCE UPDATE) DT 01-AUG-1992 (REL. 23, LAST ANNOTATION UPDATE) DT lines in a TREMBL entry: DT 01-NOV-1996 (TREMBLREL. 01, CREATED) DT 01-NOV-1996 (TREMBLREL. 01, LAST SEQUENCE UPDATE) DT 01-FEB-1997 (TREMBLREL. 02, LAST ANNOTATION UPDATE) 5. Weekly updates of TREMBL Weekly cumulative updates of TREMBL are available by anonymous FTP and from the EBI SRS server. 6. 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. SP-TREMBL is searchable on the FASTA server of the EBI and will be soon searchable on the BLITZ server of the EBI.