Assessing and improving the accuracy of detecting protein adaptation with the TreeSAAP analytical software. (11th March 2010)

• Record Type: Journal Article
• Authors: McClellan, David A.; Ellison, David D.
• Is Part Of: International journal of bioinformatics research and applications. Volume 6:Number 2(2010)
• Page Start: 120
• Page End: 133
• Publication Date: 2010-03-11
• Subjects: molecular evolution -- protein adaptation -- TreeSAAP -- MM01 -- simulation -- protein-coding DNA sequences -- positive selection -- negative selection -- accuracy -- bioinformatics -- amino acid replacement -- false positives; Bioinformatics -- Periodicals; 570.285
• Languages: English
• ISSNs: 1744-5485

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.