A new Perl toolkit for the detection and analysis of polymorphic loci and their application for bacterial typing

Since the introduction of DNA fingerprinting during the 1990s, molecular typing has been extensively employed in human medicine, veterinary medicine 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. Loci employed for bacterial typing include Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), Variable Number of Tandem Repeats (VNTR) and Simple Sequence Repeats (SSR) among others. Hitherto, several tools have been developed for the detection and comparison of such loci and some information systems have been developed either locus-specific or organism-specific.
Here, we present 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 and group extension and comparison of any locus definable with the supported rules. We successfully employed the library for the analysis of VNTRs as a test case on genomes of different qualities from the genus Xanthomonas, a group of plant pathogens belonging to the gamma division of Proteobacteria. We used the library to reproduce and automate a previous workflow that required high human intervention, without losing results quality and reducing the risk of human error.
The tool is accessible at http://bionfo-prod.mpl.ird.fr/xantho/ and is being used for the development of laboratory genotyping tools of the xanthomonads.

No relevant conflicts of interest declared.