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Bioinformatics Advance Access originally published online on September 13, 2005
Bioinformatics 2005 21(22):4190-4191; doi:10.1093/bioinformatics/bti678
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

BADASP: predicting functional specificity in protein families using ancestral sequences

Richard J. Edwards * and Denis C. Shields

Clinical Pharmacology, The Royal College of Surgeons in Ireland 123 St Stephen's Green, Dublin 2, Ireland

*To whom correspondence should be addressed.

Summary: 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.

Availability: BADASP is freely available from http://www.bioinformatics.rcsi.ie/~redwards/badasp/

Contact: redwards{at}rcsi.ie

Supplementary information: A manual with further details can be downloaded from http://www.bioinformatics.rcsi.ie/~redwards/badasp/

Received on August 2, 2005; revised on September 6, 2005; accepted on September 12, 2005

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