The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000

2000 | Amos Bairoch* and Rolf Apweiler1
SWISS-PROT is a curated protein sequence database that provides high-quality annotations, including function, domain structure, post-translational modifications, and more. It aims to minimize redundancy and integrate with other databases. TrEMBL, a computer-annotated supplement, includes entries derived from translating all coding sequences (CDSs) in the EMBL database, excluding those already in SWISS-PROT. The Human Proteomics Initiative (HPI) is a major project to annotate all known human sequences according to SWISS-PROT standards. SWISS-PROT is available at http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/. SWISS-PROT is a collaborative effort between the EMBL and the Swiss Institute of Bioinformatics (SIB). It distinguishes itself through annotations, minimal redundancy, and integration with other databases. Annotations include function, post-translational modifications, domains, secondary and quaternary structures, similarities to other proteins, diseases, and sequence variants. SWISS-PROT uses comment lines, feature tables, and keyword lines for annotations. It minimizes redundancy by merging data from different sources and indicates conflicts in the feature table. SWISS-PROT is integrated with other databases through cross-references, allowing users to access nucleic acid sequences, disease descriptions, 3D structures, and protein family information. Recent developments include format and content enhancements, new documentation, and improved cross-references. The database now includes 81,000 sequence entries, abstracted from ~65,000 references, with 30 million amino acids. TrEMBL, introduced in 1996, provides computer-annotated entries from EMBL CDSs not in SWISS-PROT. TrEMBL release 11 includes 245,761 entries, with SP-TrEMBL containing 199,794 entries to be incorporated into SWISS-PROT. REM-TrEMBL contains entries not to be included in SWISS-PROT. TrEMBL uses rule-based systems to improve annotations and reduce redundancy. SWISS-PROT is free for academic users, with annual subscription fees for commercial users. It is distributed on CD-ROM and available via anonymous FTP. Users can submit data or updates to SWISS-PROT via email or the web. SWISS-PROT is released four times a year, with weekly updates. Non-redundant data sets are provided weekly. Swiss-Shop is an automated system for sequence alerts. SWISS-PROT and TrEMBL are available at http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/.SWISS-PROT is a curated protein sequence database that provides high-quality annotations, including function, domain structure, post-translational modifications, and more. It aims to minimize redundancy and integrate with other databases. TrEMBL, a computer-annotated supplement, includes entries derived from translating all coding sequences (CDSs) in the EMBL database, excluding those already in SWISS-PROT. The Human Proteomics Initiative (HPI) is a major project to annotate all known human sequences according to SWISS-PROT standards. SWISS-PROT is available at http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/. SWISS-PROT is a collaborative effort between the EMBL and the Swiss Institute of Bioinformatics (SIB). It distinguishes itself through annotations, minimal redundancy, and integration with other databases. Annotations include function, post-translational modifications, domains, secondary and quaternary structures, similarities to other proteins, diseases, and sequence variants. SWISS-PROT uses comment lines, feature tables, and keyword lines for annotations. It minimizes redundancy by merging data from different sources and indicates conflicts in the feature table. SWISS-PROT is integrated with other databases through cross-references, allowing users to access nucleic acid sequences, disease descriptions, 3D structures, and protein family information. Recent developments include format and content enhancements, new documentation, and improved cross-references. The database now includes 81,000 sequence entries, abstracted from ~65,000 references, with 30 million amino acids. TrEMBL, introduced in 1996, provides computer-annotated entries from EMBL CDSs not in SWISS-PROT. TrEMBL release 11 includes 245,761 entries, with SP-TrEMBL containing 199,794 entries to be incorporated into SWISS-PROT. REM-TrEMBL contains entries not to be included in SWISS-PROT. TrEMBL uses rule-based systems to improve annotations and reduce redundancy. SWISS-PROT is free for academic users, with annual subscription fees for commercial users. It is distributed on CD-ROM and available via anonymous FTP. Users can submit data or updates to SWISS-PROT via email or the web. SWISS-PROT is released four times a year, with weekly updates. Non-redundant data sets are provided weekly. Swiss-Shop is an automated system for sequence alerts. SWISS-PROT and TrEMBL are available at http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/.
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