A non-parametric method for detecting specificity determining sites in protein sequence alignments. Specificity determining sites (SDSs) in alignments of protein sequences are sites at which subfamilies of the aligned sequences have been under differential selective pressure. Identifying SDSs is important because they are key in understanding the functional specificity of each subfamily. Differential selection at an SDS will result in differences between subfamilies in the distribution of amino-acids at that site. However, statistical analysis of such differences is complicated by phylogenetic relationships within each subfamily, which profoundly influence these differences. We develop a non-parametric approach to evaluating purely statistical SDS evidence in a sequence alignment, taking account of phylogeny through a novel tree-respecting randomisation based on the principle of parsimony. Our approach does not exploit bioinformatic measures based on amino-acid properties or rates of evolution, as do other methods. Our intention is thereby to supplement and strengthen other methods of SDS prediction, not to compete with them. Our methodology is implemented in the R package called SDSparsimony, freely downloadable from wally.gilks/SDSparsimonyPackage/Welcome.html.

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