In this process, a stretch of nucleotides is duplicated to produce two or more adjacent copies, resulting in a tandem repeat. Over time, the copies undergo additional mutations so that typically, multiple approximate tandem copies are present. Tandem repeats occur frequently in the human genome, including the centromeres and telomeres which are important chromosomal components. They have been shown to cause inherited human diseases, may play a variety of regulatory and evolutionary roles, and because of their polymorphic character, are important laboratory tools for linkage analysis and DNA fingerprinting. In this talk I will discuss an efficient algorithm for detecting tandem repeats in genomic sequence data.
Detection is based on k-tuple matching and a collection of statistical filtering criteria.
This involves using the pattern of mutations among the copies to determine a minimal or a most likely history for the repeat. A history tries to describe the interwoven pattern of duplication and mutation events in such a way as to minimize the number of identical mutations that arise independently. In this talk I will also describe approaches to algorithmic reconstruction of a tandem repeat history.