UniProt: the Universal Protein Knowledgebase

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UniProt: the Universal Protein Knowledgebase (2004)

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by Rolf Apweiler , Amos Bairoch , Cathy H. Wu , Winona C. Barker , Brigitte Boeckmann , Serenella Ferro , Elisabeth Gasteiger , Hongzhan Huang , Rodrigo Lopez , Michele Magrane , Maria J. Martin , Darren A. Natale , Claire O'Donovan , Nicole Redaschi , Lai-Su L. Yeh

Venue:	NUCLEIC ACIDS RES
Citations:	335 - 27 self

Citations

1069	The Pfam protein families database - Bateman, Coin, et al. (Show Context) Citation Context ... all protein sequences in UniProt into families and superfamilies. InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam =-=(11),-=- PROSITE (12), PRINTS (13), ProDom (14), SMART (15), PIRSF (16), Superfamily (17) and TIGRFAMs (18). The comprehensive InterPro classi®cation is a prerequisite for improving the quality and quantity ...
747	The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. - Boeckmann, Bairoch, et al. - 2003 (Show Context) Citation Context ...prot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scienti®c community is encouraged to submit data for inclusion in UniProt. INTRODUCTION Until recently, Swiss-Prot + TrEMBL=-= (1)-=- and PIR-PSD (2) coexisted as protein databases with differing sequence coverage and annotation priorities. In 2002, the Swiss-Prot + TrEMBL group at the Swiss Institute of Bioinformatics (SIB) and Eu...
388	RefSeq and LocusLink: NCBI gene-centered resources - Pruitt, Maglott - 2001 (Show Context) Citation Context ...available. It contains publicly available protein sequences from many different sources, including Swiss-Prot, TrEMBL, PIR-PSD, EMBL (3), Ensembl (4), IPI (http://www.ebi.ac.uk/ IPI), PDB (5), RefSeq =-=(6),-=- FlyBase (7), WormBase (8), and European, American and Japanese patent of®ces. While a protein sequence may exist in multiple databases and more than once in a given database, UniParc stores each uni...
312	The Ensembl genome database project - Hubbard, Barker, et al. - 2002 (Show Context) Citation Context ... accessible non-redundant protein sequence collection available. It contains publicly available protein sequences from many different sources, including Swiss-Prot, TrEMBL, PIR-PSD, EMBL (3), Ensembl =-=(4),-=- IPI (http://www.ebi.ac.uk/ IPI), PDB (5), RefSeq (6), FlyBase (7), WormBase (8), and European, American and Japanese patent of®ces. While a protein sequence may exist in multiple databases and more ...
238	The InterPro Database, 2003 brings increased coverage and new features - Mulder, Apweiler, et al. - 2003 (Show Context) Citation Context ...on are required. One promising approach is automatic large-scale functional characterization and annotation, which is generated with limited human interaction. InterPro classi®cation. We use InterPro=-= (10)-=- to recognize domains and to classify all protein sequences in UniProt into families and superfamilies. InterPro is an integrated resource of protein families, domains and sites that amalgamates the e...
203	C.: Assignment of homology to genome sequences using a library of hidden markov models that represent all proteins of known structure - Gough, Karplus, et al. - 2001 (Show Context) Citation Context ...integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (11), PROSITE (12), PRINTS (13), ProDom (14), SMART (15), PIRSF (16), Superfamily =-=(17) a-=-nd TIGRFAMs (18). The comprehensive InterPro classi®cation is a prerequisite for improving the quality and quantity of our annotation using highly structured, classi®cation-driven, rule-based, autom...
154	Recent improvements to the SMART domain-based sequence annotation resource. - Letunic, Goodstadt, et al. - 2002 (Show Context) Citation Context ...superfamilies. InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (11), PROSITE (12), PRINTS (13), ProDom (14), SMART =-=(15), -=-PIRSF (16), Superfamily (17) and TIGRFAMs (18). The comprehensive InterPro classi®cation is a prerequisite for improving the quality and quantity of our annotation using highly structured, classi®ca...
122	Recent improvements to the PROSITE database. - Hulo, Sigrist, et al. - 2004 (Show Context) Citation Context ...equences in UniProt into families and superfamilies. InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (11), PROSITE =-=(12),-=- PRINTS (13), ProDom (14), SMART (15), PIRSF (16), Superfamily (17) and TIGRFAMs (18). The comprehensive InterPro classi®cation is a prerequisite for improving the quality and quantity of our annotat...
112	its automatic supplement, prePRINTS - TK, Bradley, et al. (Show Context) Citation Context ...niProt into families and superfamilies. InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (11), PROSITE (12), PRINTS =-=(13),-=- ProDom (14), SMART (15), PIRSF (16), Superfamily (17) and TIGRFAMs (18). The comprehensive InterPro classi®cation is a prerequisite for improving the quality and quantity of our annotation using hig...
89	ProDom: automated clustering of homologous domains. - Servant, Bru, et al. - 2002 (Show Context) Citation Context ...amilies and superfamilies. InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (11), PROSITE (12), PRINTS (13), ProDom =-=(14),-=- SMART (15), PIRSF (16), Superfamily (17) and TIGRFAMs (18). The comprehensive InterPro classi®cation is a prerequisite for improving the quality and quantity of our annotation using highly structure...
84	The Protein Data Bank and structural genomics - Westbrook, Feng, et al. (Show Context) Citation Context ... collection available. It contains publicly available protein sequences from many different sources, including Swiss-Prot, TrEMBL, PIR-PSD, EMBL (3), Ensembl (4), IPI (http://www.ebi.ac.uk/ IPI), PDB =-=(5),-=- RefSeq (6), FlyBase (7), WormBase (8), and European, American and Japanese patent of®ces. While a protein sequence may exist in multiple databases and more than once in a given database, UniParc sto...
79	The Protein Information Resource”, - Wu, Yeh, et al. - 2003 (Show Context) Citation Context ...nloaded in several formats (ftp://ftp.uniprot.org/pub). The scienti®c community is encouraged to submit data for inclusion in UniProt. INTRODUCTION Until recently, Swiss-Prot + TrEMBL (1) and PIR-PSD=-= (2)-=- coexisted as protein databases with differing sequence coverage and annotation priorities. In 2002, the Swiss-Prot + TrEMBL group at the Swiss Institute of Bioinformatics (SIB) and European Bioinform...
57	TIGRFAMs: a protein family resource for the functional identification of proteins. - Haft, Loftus, et al. - 2001 (Show Context) Citation Context ...e of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (11), PROSITE (12), PRINTS (13), ProDom (14), SMART (15), PIRSF (16), Superfamily (17) and TIGRFAMs =-=(18). -=-The comprehensive InterPro classi®cation is a prerequisite for improving the quality and quantity of our annotation using highly structured, classi®cation-driven, rule-based, automated procedures. A...
49	WormBase: A cross-species database for comparative genomics. - Harris, Lee, et al. - 2003 (Show Context) Citation Context ...icly available protein sequences from many different sources, including Swiss-Prot, TrEMBL, PIR-PSD, EMBL (3), Ensembl (4), IPI (http://www.ebi.ac.uk/ IPI), PDB (5), RefSeq (6), FlyBase (7), WormBase =-=(8),-=- and European, American and Japanese patent of®ces. While a protein sequence may exist in multiple databases and more than once in a given database, UniParc stores each unique sequence only once and ...
47	Automated annotation of microbial proteomes in SWISS-PROT - Gattiker, Michoud, et al. - 2003 (Show Context) Citation Context ... and Manual Annotation of microbial Proteomes (HAMAP) A combined approach of automated and manual annotation for prokaryotic genomes in Swiss-Prot has resulted in the development of the HAMAP project =-=(21)-=-. The HAMAP project, or `High-quality Automated and Manual Annotation of microbial Proteomes' aims to integrate manual and automatic annotation methods in order to enhance the speed of the curation pr...
33	The EMBL nucleotide sequence database: major new developments - Stoesser, Baker, et al. (Show Context) Citation Context ...sive publicly accessible non-redundant protein sequence collection available. It contains publicly available protein sequences from many different sources, including Swiss-Prot, TrEMBL, PIR-PSD, EMBL =-=(3),-=- Ensembl (4), IPI (http://www.ebi.ac.uk/ IPI), PDB (5), RefSeq (6), FlyBase (7), WormBase (8), and European, American and Japanese patent of®ces. While a protein sequence may exist in multiple databa...
12	VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL - Kersey, Hermjakob, et al. - 2000 (Show Context) Citation Context ...icated in the feature table of the corresponding UniProt entry. Splice isoforms may differ considerably from one another, with potentially <50% sequence similarity between isoforms. The tool VARSPLIC =-=(22),-=- which is freely available enables the recreation of all annotated splice variants from the FT of a UniProt entry, or for the complete database. A FASTAformatted ®le containing all splice variants an...
9	Gene Ontology: tool for the uni®cation of biology - Ashburner, Ball, et al. - 2000 (Show Context) Citation Context ... annotation described above, all UniProt curators read a large amount of scienti®c literature related to each protein. This enables them to contribute to the work of the gene ontology (GO) consortium=-= (9)-=- by assigning GO terms during the annotation process as they extract information related to each of the GO ontologies, i.e. the function of a protein, what processes it is involved in and where in the...
9	A novel method for automatic and reliable functional annotation - Fleischmann, Moeller, et al. - 1999 (Show Context) Citation Context ...or automatic annotation, a novel system of standardized transfer of annotation from well-characterized proteins in the Swiss-Prot section of UniProt to non-annotated TrEMBL entries has been developed =-=(19)-=-. Using this system, the Swiss-Prot section is used as the source to generate the annotation rules, which are then stored and managed in RuleBase. InterPro is then used to assign TrEMBL entries into g...
4	Protein family classi®cation and functional annotation - Wu, Huang, et al. - 2003 (Show Context) Citation Context ...also been used to detect and correct numerous genome annotation errors that have resulted from identi®cations based only on local domain similarities and subsequently propagated based on transitivity=-= (20)-=-. High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) A combined approach of automated and manual annotation for prokaryotic genomes in Swiss-Prot has resulted in the developme...
1	PIRSF: family classi®cation system at the Protein Information Resource - Wu, Nikolskaya, et al. - 2004 (Show Context) Citation Context ...s. InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (11), PROSITE (12), PRINTS (13), ProDom (14), SMART (15), PIRSF =-=(16), -=-Superfamily (17) and TIGRFAMs (18). The comprehensive InterPro classi®cation is a prerequisite for improving the quality and quantity of our annotation using highly structured, classi®cation-driven,...
1	Tolerating some redundancy signi®cantly speeds up clustering of large protein databases - Li, Jaroszewski, et al. - 2002 (Show Context) Citation Context ...m the same source organism. An example NREF100 report can be found at http://www.pir.uniprot.org/cgi-bin/unipEntry?id= URI0000E815. NREF90 and NREF50 are built from NREF100 using the CD-HIT algorithm =-=(23) -=-to provide non-redundant sequence collections for the scienti®c user community to perform faster homology searches. All records from all source organisms with mutual sequence identity of >90% or >50%...