Fast Structured Motif Search in DNA Sequences

We study the problem of structured motif search in DNA sequences. This is a fundamental task in bioinformatics which contributes to better understanding of genome characteristics and properties. We propose an efficient algorithm for Exact Match, Overlapping Structured motif search (EMOS), which uses a suffix tree index we proposed earlier and runs on a typical desktop computer. We have conducted numerous experiments to evaluate EMOS and compared its performance with the best known solution, SMOTIF1 [1]. While in some cases the search time of EMOS is comparable to SMOTIF1, it is on average 5 to 6 times faster.

• Type: Conference
• Year: 2008
• Where: BIRD
• Authors: Mihail Halachev, Nematollaah Shiri
• Keywords: Bioinformatics, BIRD 2008, EMOS, Structured Motif Search, Suffix Tree Index