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

Online publication date: Wed, 10-Mar-2010

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