title: PenBase, the shrimp antimicrobial peptide penaeidin database: sequence-based classification and recommended nomenclature.
abstract: Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at , has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature.
authors.affiliation: Ifremer-CNRS-University of Montpellier 2, UMR 5171 Génome Population Interaction Adaptation, 2 Place E. Bataillon, CC80, F-34095 Montpellier cedex 5, France. ygueguen@ifremer.fr
authors.forename: Yannick
authors.initials: Y
authors.lastname: Gueguen
authors.forename: Julien
authors.initials: J
authors.lastname: Garnier
authors.forename: Lorenne
authors.initials: L
authors.lastname: Robert
authors.forename: Marie-Paule
authors.initials: MP
authors.lastname: Lefranc
authors.forename: Isabelle
authors.initials: I
authors.lastname: Mougenot
authors.forename: Julien
authors.initials: J
authors.lastname: de Lorgeril
authors.forename: Michael
authors.initials: M
authors.lastname: Janech
authors.forename: Paul S
authors.initials: PS
authors.lastname: Gross
authors.forename: Gregory W
authors.initials: GW
authors.lastname: Warr
authors.forename: Brandon
authors.initials: B
authors.lastname: Cuthbertson
authors.forename: Margherita A
authors.initials: MA
authors.lastname: Barracco
authors.forename: Philippe
authors.initials: P
authors.lastname: Bulet
authors.forename: André
authors.initials: A
authors.lastname: Aumelas
authors.forename: Yinshan
authors.initials: Y
authors.lastname: Yang
authors.forename: Dong
authors.initials: D
authors.lastname: Bo
authors.forename: Jianhai
authors.initials: J
authors.lastname: Xiang
authors.forename: Anchalee
authors.initials: A
authors.lastname: Tassanakajon
authors.forename: David
authors.initials: D
authors.lastname: Piquemal
authors.forename: Evelyne
authors.initials: E
authors.lastname: Bachère
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000145:classification* / Q000378:metabolism; D030562:Databases, Protein; D033364:Decapoda / Q000737:chemistry*; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry* / Q000145:classification* / Q000378:metabolism; D016415:Sequence Alignment; D009626:Terminology as Topic
chemical_list: D000900:Anti-Bacterial Agents; D010455:Peptides