BADASP: predicting functional specificity in protein families using ancestral sequences.
CONCLUSIONS
Burst After Duplication with Ancestral Sequence Predictions (BADASP) is a software package for identifying sites that may confer subfamily-specific biological functions in protein families following functional divergence of duplicated proteins. A given protein phylogeny is grouped into subfamilies based on orthology/paralogy relationships and/or user definitions. Ancestral sequences are then predicted from the sequence alignment and the functional specificity is calculated using variants of the Burst After Duplication method, which tests for radical amino acid substitutions following gene duplications that are subsequently conserved. Statistics are output along with subfamily groupings and ancestral sequences for an easy analysis with other packages.


BACKGROUND
BADASP is freely available from http://www.bioinformatics.rcsi.ie/~redwards/badasp/
Edwards
Richard J
RJ
Clinical Pharmacology, The Royal College of Surgeons in Ireland, Dublin. redwards@rcsi.ie
Shields
Denis C
DC
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D001330:Electronic Data Processing; D015233:Models, Statistical; D005810:Multigene Family; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry*; D012680:Sensitivity and Specificity; D020539:Sequence Analysis, Protein; D012984:Software
D000596:Amino Acids; D011506:Proteins