Assessing and improving the accuracy of detecting protein adaptation with the TreeSAAP analytical software Online publication date: Wed, 10-Mar-2010
by David A. McClellan, David D. Ellison
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 6, No. 2, 2010
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.
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