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

De Oliveira Lima, Tania; Auchincloss Damay, Andréa; Coudert, Elisabeth; Keller, Guillaume Bertrand; Michoud, Karine Florence; Rivoire, Catherine; Bulliard, Virginie; De Castro, Eduardo; Lachaize, Corinne; Baratin, Delphine; Phan, Isabelle; Bougueleret, Lydie; Bairoch, Amos Marc

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Title		HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot
Authors		De Oliveira Lima, Tania Auchincloss Damay, Andréa Coudert, Elisabeth Keller, Guillaume Bertrand Michoud, Karine Florence Rivoire, Catherine Bulliard, Virginie De Castro, Eduardo Lachaize, Corinne Baratin, Delphine Phan, Isabelle Bougueleret, Lydie Bairoch, Amos Marc show all authors [1 - 13]
Published in		Nucleic Acids Research. 2009, vol. 37, no. Database issue, p. D471-8
Abstract		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).
Keywords		Archaeal Proteins/chemistry/classification/genetics — Bacterial Proteins/chemistry/classification/genetics — Databases, Protein — Genomics — Proteome/chemistry — Proteomics — Sequence Alignment — Sequence Analysis, Protein — Software
Identifiers		DOI: 10.1093/nar/gkn661 PMID: 18849571
Full text		Article (Author postprint) (2.9 MB) - Free access Other version: http://nar.oxfordjournals.org/cgi/content/full/37/suppl_1/D471
Structures		Faculté de médecine / Section de médecine fondamentale / Département de biologie structurale et bioinformatique
Research group		Calipho (80)
Citation (ISO format)		DE OLIVEIRA LIMA, Tania et al. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. In: Nucleic Acids Research, 2009, vol. 37, n° Database issue, p. D471-8. https://archive-ouverte.unige.ch/unige:1418