Tandem repeats finder: a program to analyze DNA sequences

A tandem repeat in DNA is two or more contiguous, approximate copies of a p attern of nucleotides. Tandem repeats have been shown to cause human diseas e, may play a variety of regulatory and evolutionary roles and are importan t laboratory and analytic tools. Extensive knowledge about pattern size, co py number, mutational history, etc. for tandem repeats has been limited by the inability to easily detect them in genomic sequence data. In this paper , we present a new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size. We model tandem re peats by percent identity and frequency of indels between adjacent pattern copies and use statistically based recognition criteria. We demonstrate the algorithm's speed and its ability to detect tandem repeats that have under gone extensive mutational change by analyzing four sequences: the human fra taxin gene, the human beta T cell receptor locus sequence and two yeast chr omosomes. These sequences range in size from 3 kb up to 700 kb, A World Wid e Web server interface at c3.biomath.mssm.edu/trf.html has been established for automated use of the program.