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Bioinformatics Advance Access published online on March 6, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm068
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

AMPer: A Database and an Automated Discovery Tool for Antimicrobial Peptides.

Christopher D. Fjell 1,*, Robert E.W. Hancock 2 and Artem Cherkasov 1

1Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, University of British Columbia, 2733 Heather street, Vancouver, BC, Canada, V5Z 3J5, Canada
2Centre for Microbial Diseases and Immunity Research, University of British Columbia, #2259 Lower Mall Research Station, Vancouver, British Columbia, V6T 1Z3, Canada

*To whom correspondence should be addressed. Christopher Fjell, E-mail: cfjell{at}interchange.ubc.ca, chris.fjell{at}similistech.ca


  Abstract

Motivation: Increasing antibiotics resistance in human pathogens represents a pressing public health issue worldwide for which novel antibiotic therapies based on antimicrobial peptides (AMPs) may offer one possible solution. In the current study we utilized publicly available data on AMPs to construct hidden Markov models (HMMs) that enable recognition of individual classes of antimicrobials peptides (such as defensins, cathelicidins, cecropins, etc) with up to 99% accuracy and can be used for discovering novel AMP candidates.

Results: HMM models for both mature peptides and propeptides were constructed. A total of 146 models for mature peptides and 40 for propeptides have been developed for individual AMP classes. These were created by clustering and analyzing AMP sequences available in the public sources and by consequent iterative scanning of the Swiss-Prot database for previously unknown gene-coded AMPs. As a result, an additional 229 addtional AMPs have been identified from Swiss-Prot, and all but 34 could be associated with known antimicrobial activities according to the literature. The final set of 1045 mature peptides and 253 propeptides have been organized into the open-source AMPer database.

Availability: The developed HMM-based tools and AMP sequences can be accessed through the AMPer resource at http://www.cnbi2.com/cgi-bin/amp.pl.

Associate Editor: Prof. Martin Bishop

Received on May 29, 2006; revised on January 23, 2007; accepted on February 22, 2007

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