The Prague Stringology Conference 2003

Richard Groult, Martine Leonard and Laurent Mouchard

A Linear Algorithm for the Detection of Evolutive Tandem Repeats

We present here a linear algorithm for the detection of evolutive tandem repeats. An evolutive tandem repeat consists in a series of almost contiguous copies, every copy being similar (using Hamming distance in this article) to its predecessor and successor. From a global view point, evolutive tandem repeats extend the traditional approximate tandem repeat where each copy has to be in a neighborhood of a given model. Due to the lack of algorithms, these repeats have been discovered in genomic sequences only recently. In this article, we present a two-stage algorithm, where we first compute an array containing all the Hamming distances between candidates, then we visit this array to build a complete evolutive tandem repeat from insulated pairs of copies. Moreover, we explain how it is still consistent with the usual technique devoted to dynamic programming which consists in filling a comparison matrix and backtracking through it to find an optimal alignment.

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