SWISS-PROT & TREMBL THE SWISS-PROT PROTEIN SEQUENCE DATA BANK SWISS-PROT is an annotated protein sequence database established in 1986 and maintained collaboratively, since 1987, by the group of Amos Bairoch first at the Department of Medical Biochemistry of the University of Geneva and now at the Swiss Institute of Bioinformatics (SIB) and the EMBL Data Library (now the EMBL Outstation - The European Bioinformatics Institute (EBI)). The SWISS-PROT protein sequence data bank consists of sequence entries. Sequence entries are composed of different lines types, each with their own format. For standardization purposes the format of SWISS-PROT follows as closely as possible that of the EMBL Nucleotide Sequence Database. Organizations Swiss Institute of Bioinformatics The EMBL Outstation - The European Bioinformatics Institute (EBI) FTP addresses ftp://ftp.expasy.ch/databases/swiss-prot ftp://ftp.ebi.ac.uk/databases/swiss-prot WWW server: http://www.expasy.ch/, http://www.ebi.ac.uk/ Electronic mail address:: swiss-prot@expasy.ch TREMBL - 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. Since we do not want to dilute the quality standards of SWISS-PROT by incorporating sequences into the database without proper sequence analysis and annotation, we cannot speed up the incorporation of new incoming data indefinitely. But as we also want to make the sequences available as fast as possible, we have introduced with SWISS-PROT a computer annotated supplement. This supplement consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except those already included in SWISS-PROT. We name this supplement TrEMBL (Translation from EMBL). It can be considered as a preliminary section of SWISS-PROT. This SWISS-PROT release is supplemented by TrEMBL release 6. TrEMBL is split in two main sections; SP-TrEMBL and REM-TrEMBL: - SP-TrEMBL (SWISS-PROT TrEMBL) contains the entries (150'329 in release 6) which should be incorporated into SWISS-PROT. SWISS-PROT accession numbers have been assigned for all SP-TrEMBL entries. - REM-TrEMBL (REMaining TrEMBL) contains the entries (27'428 in release 6) that we do not want to include in SWISS-PROT for a variety of reasons (synthetic sequences, pseudogenes, translations of uncorrect open reading frames, fragments with less than eight amino acids, patent-derived sequences, immunoglobulins and T-cell receptors, etc.) TrEMBL is available by FTP from the EBI server (ftp.ebi.ac.uk) in the directory '/pub/databases/trembl'. It can be queried on WWW by the EBI SRS server (http://www.ebi.ac.uk/). It is also available on the SWISS-PROT CD- ROM and is searchable on the FASTA, BIC and BLAST servers of the EBI. If you want to cite SWISS-PROT 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). IMPORTANT ANNOUNCEMENT It became obvious in the last years that the tremendous increase in data flow has created a requirement for resources which cannot be addressed in full by public funding. This is causing databases to fall behind the research. We believe that the only solution to the resource shortfall is to ask commercial users to participate by paying a license fee. No fee will be charged to academic users, nor will any restriction be imposed on their use or reuse of the data. both SWISS-PROT and PROSITE are concerned by these changes while this is not the case of ENZYME. A document fully describing what will be the impact of this change for SWISS-PROT is available with the SWISS-PROT distribution files on FTP (SP_98.TXT). You can also access the document as well as other relevant ones from: http://www.expasy.ch/announce/ http://www.ebi.ac.uk/news.html If you do not have the time to read this document, the most important take-home message is that these changes should not have any impact on the way SWISS-PROT or PROSITE are accessed or redistributed. Academic users will not be affected by these changes. Industrial end-users will also not directly be affected as long as their employer pays the license fee. The same holds true for bioinformatics companies. Academic software or database developers as well as providers of database distribution services will be only minimally affected by these changes. We hope to be able to ensure their long-term financial survival. We sincerely hope and believe that in the next two years the only change that will matter will be the increase in scope and timeliness of the databases. Finally, it should be noted that release 36 of SWISS-PROT and release 15 of PROSITE are not concerned by these changes. There are no restrictions on their use and their distribution.