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An Experimental Comparison of PMSPrune and Other Algorithms for Motif Search by Sharma, Dolly; Rajasekaran, Sanguthevar; Dinh, Hieu is a scholarly article available to read on EtoBox.

What is An Experimental Comparison of PMSPrune and Other Algorithms for Motif Search about?

Extracting meaningful patterns from voluminous amount of biological data is a very big challenge. Motifs are biological patterns of great interest to biologists. Many different versions of the motif finding problem have been identified by researchers. Examples include the Planted $(l, d)$ Motif version, those based on position-specific score matrices, etc. A comparative study of the various motif search algorithms is very important for several reasons. For example, we could identify the strengths and weaknesses of each. As a result, we might be able to devise hybrids that will perform better than the individual components. In this paper we (either directly or indirectly) compare the performance of PMSprune (an algorithm based on the $(l, d)$ motif model) and several other algorithms in terms of seven measures and using well established benchmarks In this paper, we (directly or indirectly) compare the quality of motifs predicted by PMSprune and 14 other algorithms. We have employed several benchmark datasets including the one used by Tompa, et.al. These comparisons show that the performance of PMSprune is competitive when compared to the other 14 algorithms tested. We have compared

Author

Sharma, Dolly; Rajasekaran, Sanguthevar; Dinh, Hieu

Published

2011

Language

EN