Abstract
BackgroundTandem repeat arrays showing variation between sequences within a population, between strains or across species may have functional effects. The increasing availability of genomic sequence data makes routine description of observed variation possible, creating a need for tools to describe such variability.ResultsWe present a set of programs that facilitate the identification of tandem repeats showing variation across multiple sequences or genomes, and the prediction of potentially polymorphic tandem repeats. The VNTRfinder (Variable Number of Tandem Repeats finder) program enables the detection of sequence length variation between arrays of inter-specific or intra-specific tandem repeats. In the absence of comparable sequences to explore observed variation, predictions are provided describing which tandem repeats are more likely to be variable, to help guide and focus further experimental evaluation.ConclusionThese tools represent a resource for researchers interested in tandem repeats in nucleotide sequences that are most likely to be of clinical and evolutionary interest. The tools are available at . Downloadable versions for UNIX/LINUX and WINDOWS which permit the consideration of longer and more numerous sequences are also available.
Highlights
Tandem repeat arrays showing variation between sequences within a population, between strains or across species may have functional effects
The first observation (Table 1) is that for the repeats that were successfully matched by both methods in Mycobacterium tuberculosis, they agreed quite strongly in their definition of whether or not they were variant (95% of Denoeud variants were classed as variants by VNTRfinder; Table 2 (the percentage is 62% (72/116) for VNTRfinder variants classified as variants by the Denoeud method
For the more distantly related Neisseria meningitidis comparison, VNTRfinder again matches more repeats (69% versus 51% matched by the Denoeud method) (Table 1)
Summary
Tandem repeat arrays showing variation between sequences within a population, between strains or across species may have functional effects. The identification of tandem repeats exhibiting or with the potential to exhibit length variation is of considerable importance to medical and evolutionary-based research. Denoeud and Vergnaud [1] have described a web-based resource [2], which displays precomputed tandem repeat length variations among bacterial strains. Another resource is TRDB, Tandem Repeats Database [3]. This versatile resource allows users to upload sequences, detect tandem repeats using the Tandem Repeats Finder algorithm and perform actions such as extracting flanking sequences and predicting primer sequences. We present software that allows users to upload and detect tandem repeats, but that is primarily concerned with the prediction and detec-
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