A software tool for the selection of tandem repeats for MLVA analysis

DNA fingerprinting is a reliable tool for identifying, tracing and characterizing bacterial clonal population structure. A recent technique is given by the Multiple Loci VNTR Analysis (MLVA), where VNTR denotes Variable Number of Tandem Repeats, that meets the need for fast and reliable typing methods by combining the polymorphic nature of tandem repeats (TR) and the use of Polymerase Chain Reaction (PCR) methodology. The key point in the MLVA technique is the selection of a set of TRs which have a sufficient variability (polymorphism) across strains, in order to allow easy strain typing. In this work, we present a program which analyses a set of N genomes and outputs the list of shared TRs and associated information. The program compares the TRs for each possible genome pair, and finds the sets of TRs that are shared by at least M genomes. The subsequent determination of “virtual amplicons” enables the user to consider the actual polymorphism exhibited by the different strains with regards to each given TR, which is the critical parameter for the experimental strain typing.