Comparative Analysis of Similarity Check Mechanism for Motif Extraction
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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 sensitiv
Keywords
QA75 Electronic computers. Computer science