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Bioinformatics Advance Access originally published online on March 4, 2009
Bioinformatics 2009 25(9):1187-1188; doi:10.1093/bioinformatics/btp127
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

LOCP—locating pilus operons in Gram-positive bacteria

Ilya Plyusnin 1, Liisa Holm 1,2 and Matti Kankainen 1,*

1Institute of Biotechnology and 2Department of Biological and Environmental Sciences, University of Helsinki, P.O.Box 56 (Viikinkaari 5), FIN-00014 University of Helsinki, Finland

*To whom correspondence should be addressed.


  Abstract

Summary: Pilus operons encode a pivotal host–microbe interaction structure that is vital for pathogenicity, colonization and adhesion. LOCP is a computational tool to quickly test whether or not the genome of a Gram-positive bacterium of interest or some DNA-contig in a metagenomic sample hold pilus operons. Predictions are made based on distinctive motifs of pilus-related protein sequences and on the tendency of these protein sequences to occur in dense clusters. The tool showed a phenomenal accuracy and revealed that various novel, and even unexpected, Gram-positive bacteria do possess pilus operons. Thus, the tool helps us to focus the laboratory research on genes behind this important and indicative feature, and to screen for strains containing them.

Availability: Software is available at http://ekhidna.biocenter.helsinki.fi/locp/

Contact: matti.kankainen@helsinki.fi

Supplementary information:Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on December 8, 2008; revised on March 2, 2009; accepted on March 2, 2009

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