Polloc – A Perl library for polymorphic loci analyses in bacterial molecular typing studies.
Thesis, Master in Computer Sciences – Skills integration, Université Montpellier II, College of Sciences. 2011.
Since the introduction of DNA fingerprinting during the 1990s, molecular typing has been extensively employed in medicine (for both human and non-human animals) and plant pathology for a wide range of pathogens and based on distinct polymorphic loci. The explosion of genomic data during the last decade empowered the rational design and development of typing techniques enabling the prediction and detection of specific loci with different key features, like sequence similarity, repetitive regions or domains architecture. Hitherto, several tools have been developed for the detection and comparison of the various loci employed in molecular typing, and some information systems have been developed either locus-specific or organism-specific. Here we present Polloc, a Perl library and a set of scripts for the analysis of variable loci used for bacterial typing based on highly customizable rules. The library allows the detection, grouping, group extension and comparison of any locus definable with the supported rules. We successfully employed the library for the development of Polloc-V, a tool for the analysis of VNTR (Variable Number of Tandem Repeats) loci. The library is available at CPAN with namespace Bio::Polloc, and the tool is available at http://biopred.net/VNTR/.