Efficient exact motif discovery.

ABSTRACT:

Motivation

The motif discovery problem consists of finding over-represented patterns in a collection of biosequences. It is one of the classical sequence analysis problems, but still has not been satisfactorily solved in an exact and efficient manner. This is partly due to the large number of possibilities of defining the motif search space and the notion of over-representation. Even for well-defined formalizations, the problem is frequently solved in an ad hoc manner with heuristics that do not guarantee to find the best motif.

Results

We show how to solve the motif discovery problem (almost) exactly on a practically relevant space of IUPAC generalized string patterns, using the p-value with respect to an i.i.d. model or a Markov model as the measure of over-representation.

SUBMITTER: Marschall T 

PROVIDER: S-EPMC2687942 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature