Filtering Tandem Repeats in DNA Sequences

A tandem repeat is a sequence of two or more contiguous, approximate copies of a pattern. Tandem repeats occur in the genomes of both eukaryotic and prokaryotic organisms. They are important in numerous fields including disease diagnosis, mapping studies, human identity testing (DNA fingerprinting), sequence homology, and population studies. Although tandem repeats have been used by biologists for many years, there are few tools available for performing an exhaustive search for all tandem repeats in a given sequence. In this paper we describe a software tool that has been implemented as a postprocessing stage for a popular tandem repeats program. This new stage allows the program to scale up for use with whole genomic sequences. The program now organizes and filters the data into a meaningful and manageable set. The output is presented as a succinct table of repeats, including several relevant statistics for each repeat.