Title: Assessing and improving the accuracy of detecting protein adaptation with the TreeSAAP analytical software

Authors: David A. McClellan, David D. Ellison

Addresses: Bigelow Laboratory for Ocean Sciences, 180 McKown Point Road, West Boothbay Harbor, ME 04575, USA. ' Department of Biomedical Engineering, 207 Clark Hall, 3400 N. Charles St., The Johns Hopkins University, Baltimore, MD 21218, USA

Abstract: TreeSAAP has been used in a variety of protein studies for detecting adaptation in terms of the physicochemical properties involved in amino acid replacement. The accuracy of TreeSAAP was here tested using simulated protein-coding DNA data. A sampling of 1402 simulated amino acid replacements resulted in a default accuracy of 81.1%, with most properties exhibiting >90% accuracy. More than half of the false-positive results were traced to just 11 of the 180 possible single-step amino acid exchanges. Overall accuracy increased as the number of magnitude partitions used in the analysis decreased. Sliding window size did not significantly affect accuracy.

Keywords: molecular evolution; protein adaptation; TreeSAAP; MM01; simulation; protein-coding DNA sequences; positive selection; negative selection; accuracy; bioinformatics; amino acid replacement; false positives.

DOI: 10.1504/IJBRA.2010.032116

International Journal of Bioinformatics Research and Applications, 2010 Vol.6 No.2, pp.120 - 133

Published online: 10 Mar 2010 *

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