title: Automated annotation of microbial proteomes in SWISS-PROT.
abstract: Large-scale sequencing of prokaryotic genomes demands the automation of certain annotation tasks currently manually performed in the production of the SWISS-PROT protein knowledgebase. 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 process while preserving the quality of the database annotation. Automatic annotation is only applied to entries that belong to manually defined orthologous families and to entries with no identifiable similarities (ORFans). Many checks are enforced in order to prevent the propagation of wrong annotation and to spot problematic cases, which are channelled to manual curation. The results of this annotation are integrated in SWISS-PROT, and a website is provided at http://www.expasy.org/sprot/hamap/.
authors.affiliation: SWISS-PROT Group, Swiss Institute of Bioinformatics, 1 rue Michel Servet, CH-1211 Geneva 4, Switzerland. gattiker@isb-sib.ch
authors.forename: Alexandre
authors.initials: A
authors.lastname: Gattiker
authors.forename: Karine
authors.initials: K
authors.lastname: Michoud
authors.forename: Catherine
authors.initials: C
authors.lastname: Rivoire
authors.forename: Andrea H
authors.initials: AH
authors.lastname: Auchincloss
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Coudert
authors.forename: Tania
authors.initials: T
authors.lastname: Lima
authors.forename: Paul
authors.initials: P
authors.lastname: Kersey
authors.forename: Marco
authors.initials: M
authors.lastname: Pagni
authors.forename: Christian J A
authors.initials: CJ
authors.lastname: Sigrist
authors.forename: Corinne
authors.initials: C
authors.lastname: Lachaize
authors.forename: Anne Lise
authors.initials: AL
authors.lastname: Veuthey
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Gasteiger
authors.forename: Amos
authors.initials: A
authors.lastname: Bairoch
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000145:classification* / Q000502:physiology*; D003628:Database Management Systems / Q000592:standards / Q000639:trends*; D030562:Databases, Protein / Q000145:classification* / Q000592:standards*; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D020543:Proteome / Q000145:classification* / Q000502:physiology*
chemical_list: D001426:Bacterial Proteins; D020543:Proteome