LOCP is an analytical tool for LOCating Pilus operons in Gram-positive bacteria.

LOCP operates in a two-step procedure:

Firstly, 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.

Secondly, chromosome regions with statistically significant clusters of hits are located using hypergeometrical distribution and Monte Carlo simulations. These regions are referred as Pilus Like Dense Regions (PLDRs).

You can analyse your sequences at the interface page or view the precompiled predictions.

For method details see the user manual and locp methods.

Source code can be downloaded here:

  1. main program: locp.pl
  2. perl module: get_orf_from_contig_v2.pm
  3. significance scoring: bootstrap.cpp
  4. all source code: LOCP.zip