Nucleic Acids Research, 2000, Vol. 28, No. 1 45-48
© 2000 Oxford University Press
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland and 1The EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include format and content enhancements, cross-references to additional databases, new documentation files and improvements to TrEMBL, a computer-annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDSs) in the EMBL Nucleotide Sequence Database, except the CDSs already included in SWISS-PROT. We also describe the Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT. SWISS-PROT is available at: http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/
* To whom correspondence should be addressed. Tel: +41 22 702 5477; Fax: +41 22 702 5502; Email: amos.bairoch@medecine.unige.ch
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|
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|
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|
|
|
|
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|
|
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|
|
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|
|
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|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
I. Alam, A. Dress, M. Rehmsmeier, and G. Fuellen Comparative homology agreement search: An effective combination of homology-search methods PNAS, September 21, 2004; 101(38): 13814 - 13819. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
 |
|
 F. Campagne, S. Neves, C.-w. Chang, L. Skrabanek, P. T. Ram, R. Iyengar, and H. Weinstein Quantitative Information Management for the Biochemical Computation of Cellular Networks Sci. Signal., August 31, 2004; 2004(248): pl11 - pl11. [Abstract] [Full Text] [PDF]
|
|
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|
|
|
|
|
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|
|
|
|
|
|
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|
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