Section: Software

Keywords : approximate repeat detection, DNA sequences.

Repseek

Participants : Frédéric Boyer, Eric Coissac [ Correspondent ] , Alain Viari.

Repseek is a program for finding approximate repeats in large DNA sequences. While there are several efficient methods for detecting strict (or almost strict) repeats, Repseek has been designed to efficiently detect approximate repeats in DNA sequences allowing for deletion and substitution scores. Repseek also uses a statistical framework to ascertain the significance of the repeats. Repseek is based on a new, space efficient, implementation of the Karp-Miller-Rosenberg algorithm. It has been developed, through a collaboration, by Guillaume Achaz at the Université Paris VI. For more information see: http://wwwabi.snv.jussieu.fr/~public/RepSeek/