LOCP--locating pilus operons in gram-positive bacteria.
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.


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


BACKGROUND
Supplementary data are available at Bioinformatics online.
Plyusnin
Ilya
I
Institute of Biotechnology, University of Helsinki, P.O.Box 56 (Viikinkaari 5), FIN-00014 University of Helsinki, Finland.
Holm
Liisa
L
Kankainen
Matti
M
D000465:Algorithms; D010861:Fimbriae, Bacterial / Q000737:chemistry*; D016680:Genome, Bacterial; D006094:Gram-Positive Bacteria / Q000235:genetics* / Q000378:metabolism; D009876:Operon / Q000235:genetics*; D012984:Software