an R package for detecting
Specificity Determining Sites
in a multiple sequence alignment
Department of Statistics, University of Leeds, UK
Statistical Genomics Group, Biomathematics and Bioinformatics,
Rothamsted Research, Harpenden, UK
A Specificity Determining Site (SDS) in a multiple sequence alignment of a protein family is a column of the alignment which is wholly or partially responsible for functional differences between subfamilies of that family.
R package SDSparsimony predicts SDSs using a phylogeny-respecting parsimony-based randomisation (Gilks and Wang, 2011). The package requires the multiple sequence alignment, the grouping of families into subgroups and the phylogeny relating these sequences.
Download R package:
Some notes on installing the package in R:
Gilks, W. and Wang, C. (2011) A Non-parametric Method for Detecting Specificity Determining Sites in
Protein Sequence Alignments. Statistical Applications in Genetics and Molecular Biology (in press).