Comparative Analysis of Similarity Check Mechanism for Motif Extraction

In this work, a comparative analysis of the similarity check mechanism used in the most effective algorithm for mining simple motifs GEMS (Gene Enrichment Motif Searching) and that used in a popular multi-objective genetic algorithm, MOGAMOD (Multi-Objective Genetic Algorithm for Motif Discovery) was done. In our previous work, we had reported the implementation of GEMS on suffix tree –Suffix Tree Gene Enrichment Motif Searching (STGEMS) and shown the linear asymptotic runtime achieved. Here, we attempt to empirically proof the high sensitivity of the resulting algorithm, STGEMS in mining motifs from challenging sequences like we have in Plasmodium falciparum. The results obtained validates the high sensitivity of the similarity check mechanism employed in GEMS and also shows that a careful deployment of this mechanism in the multi-objective genetic algorithm, improved the sensitivity level of the resulting algorithm. The end results gave us room to exhaustively mine structured motifs.