HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot

Article Article scientifique Article HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot eng 2009 author De Oliveira Lima Tania 639265 author Auchincloss Damay Andréa 29803 author Coudert Elisabeth 639263 author Keller Guillaume Bertrand 90403 author Michoud Karine Florence 88908 author Rivoire Catherine 89392 author Bulliard Virginie 699624 author De Castro Eduardo 28647 author Lachaize Corinne 639310 author Baratin Delphine 639480 author Phan Isabelle 639323 author Bougueleret Lydie 639268 author Bairoch Amos Marc 0000-0003-2826-6444 21964 D471-478 10.1093/nar/gkn661 18849571 0305-1048 http://nar.oxfordjournals.org/cgi/content/full/37/suppl_1/D471 The growth in the number of completely sequenced microbial genomes (bacterial and archaeal) has generated a need for a procedure that provides UniProtKB/Swiss-Prot-quality annotation to as many protein sequences as possible. We have devised a semi-automated system, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), that uses manually built annotation templates for protein families to propagate annotation to all members of manually defined protein families, using very strict criteria. The HAMAP system is composed of two databases, the proteome database and the family database, and of an automatic annotation pipeline. The proteome database comprises biological and sequence information for each completely sequenced microbial proteome, and it offers several tools for CDS searches, BLAST options and retrieval of specific sets of proteins. The family database currently comprises more than 1500 manually curated protein families and their annotation templates that are used to annotate proteins that belong to one of the HAMAP families. On the HAMAP website, individual sequences as well as whole genomes can be scanned against all HAMAP families. The system provides warnings for the absence of conserved amino acid residues, unusual sequence length, etc. Thanks to the implementation of HAMAP, more than 200,000 microbial proteins have been fully annotated in UniProtKB/Swiss-Prot (HAMAP website: http://www.expasy.org/sprot/hamap). Archaeal Proteins/chemistry/classification/genetics Bacterial Proteins/chemistry/classification/genetics Databases, Protein Genomics Proteome/chemistry Proteomics Sequence Alignment Sequence Analysis, Protein Software Dewey 576 136 Département de biologie structurale et bioinformatique 21E false 57 Calipho 80 Nucleic acids research 37 Database issue 45550b87-a282-4344-aebb-017362d42cd8 Article (Accepted version) Public Article.pdf 3089757 application/pdf openAccess Faculté de médecine / Section de médecine fondamentale / Département de biologie structurale et bioinformatique

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HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot	Nucleic acids research			2009	677	520

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Baratin, Delphine