LOCP is designed to LOCate putative Pilus operons in Gram-positive prokaryotes. This is done in two steps: First, pilus-related sequences are identified by hmmsearch with a carefully selected set of profile Hidden Markov Models (HMM). Each protein sequence is then labeled either with the matching HMM models, or with the null-model, if the maximum bit score of all matches is below zero. Sequences labeled with HMMs are referred as hits and those labeled with null-model as gaps. Second, chromosome regions with statistically significant clustering of hits are located using hypergeometrical distribution and Monte Carlo simulations. These regions are referred as Pilus Like Dense Regions (PLDRs).
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Bioinformatics. 2009 May 1;25(9):1187-8. doi: 10.1093/bioinformatics/btp127. Epub 2009 Mar 4.
LOCP–locating pilus operons in gram-positive bacteria.
Plyusnin I1, Holm L, Kankainen M.