A Linear Algorithm for the Detection of Evolutive Tandem Repeats

Abstra t. We present here a linear algorithm for the dete tion of evolutive tandem repeats. An evolutive tandem repeat onsists in a series of almost ontiguous opies, every opy being similar (using Hamming distan e in this arti le) to its prede essor and su essor. From a global view point, evolutive tandem repeats extend the traditional approximate tandem repeat where ea h opy has to be in a neighborhood of a given model. Due to the la k of algorithms, these repeats have been dis overed in genomi sequen es only re ently. In this arti le, we present a two-stage algorithm, where we rst ompute an array ontaining all the Hamming distan es between andidates, then we visit this array to build a omplete evolutive tandem repeat from insulated pairs of opies. Moreover, we explain how it is still onsistent with the usual te hnique devoted to dynami programming whi h onsists in lling a omparison matrix and ba ktra king through it to nd an optimal alignment.