A Graph Based Approach to Discover Conserved Regions in DNA and Protein Sequences

This paper attempts to provide a graph based approach to discover conserved regions such as motifs in either DNA or Protein sequences. The motif discovery problem has gained lot of significance in biological science over the past decade. Lately various approaches have been used successfully to discover motifs. Some of them are based on probabilistic approach and the others on a combinatorial approach. We have followed a graph-based combinatorial approach to solve this problem, in particular, using the idea of de Bruijn graphs. The de Bruijn graph has been successfully adopted to solve problems such as local alignment and DNA fragment assembly. Our method harnesses the power of the de Bruijn graph to discover the conserved regions in a DNA or protein sequence. We have found that the algorithm was successful in mining signals for larger number of sequences and at a faster rate when compared to some popular motif searching tools.