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A Comparative Analysis of Computational Motif-Detection Methods

The detection of motifs within and among families of protein sequences can provide useful information regarding the function, structure and evolution of a protein. With the increasing number of computer programs available for motif detection, a comparative evaluation of the programs from a biological perspective is warranted. This study uses a set of 20 reverse transcriptase (RT) protein sequences to test and compare the ability of 7 different computational methods to locate the ordered-series-of-motifs that are well characterized in the RT sequences. The results provide insight to biologists as to the usage, value, and reliability of the numerous methods available.