PenBase, the shrimp antimicrobial peptide penaeidin database: sequence-based classification and recommended nomenclature.
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.
Gueguen
Yannick
Y
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
Garnier
Julien
J
Robert
Lorenne
L
Lefranc
Marie-Paule
MP
Mougenot
Isabelle
I
de Lorgeril
Julien
J
Janech
Michael
M
Gross
Paul S
PS
Warr
Gregory W
GW
Cuthbertson
Brandon
B
Barracco
Margherita A
MA
Bulet
Philippe
P
Aumelas
André
A
Yang
Yinshan
Y
Bo
Dong
D
Xiang
Jianhai
J
Tassanakajon
Anchalee
A
Piquemal
David
D
Bachère
Evelyne
E
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
D000900:Anti-Bacterial Agents; D010455:Peptides