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Bioinformatics Advance Access published online on September 13, 2005
Bioinformatics, 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@oxfordjournals.org
Received August 2, 2005
Revised September 6, 2005
Accepted September 12, 2005

Applications note

BADASP: predicting functional specificity in protein families using ancestral sequences

Richard J. Edwards 1* and Denis C. Shields 1

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

* To whom correspondence should be addressed.
Richard J. Edwards, E-mail: redwards{at}rcsi.ie


  Abstract

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 functional is specificity 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 easy analysis with other packages.

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

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


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