BScEfficientExactMotifDiscovery

Implementation of an existing motif discovery algorithm in SeqAn.

Background

The goal of motif finding is the detection of novel, unknown signals in a set of sequences [1]. For example you might want to detect transcription factor binding sites in a genome, but do not know how they look like.

However, one can be quite certain, that such motifs are never conserved exactly but only approximately. This fact makes the problem difficult.

Topic

The SeqAn library contains an implementation of basic, text-book motif finding problem. However, there are recent advances in motif finding that would be a useful state-of-the-art addition to the baseline implementation.

The work by Marschal and Rahman in [2] is one example of a current algorithm.

Comments

References

• [1] Reinert K. Algorithmische Bioinformatik Kapitel: Motif finding
• [2] Marschall, Tobias, and Sven Rahmann. Efficient exact motif discovery. Bioinformatics 25.12 (2009): i356-i364.
• [3] MoSDI implementation on Google Code