BADASP: Predicting functional specificity in protein families using ancestral sequences

Richard J. Edwards; Denis C. Shields

doi:10.1093/bioinformatics/bti678

BADASP: Predicting functional specificity in protein families using ancestral sequences

Richard J. Edwards, Denis C. Shields

Research output: Contribution to journal › Article › peer-review

21 Citations (Scopus)

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 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.

Original language	English
Pages (from-to)	4190-4191
Number of pages	2
Journal	Bioinformatics
Volume	21
Issue number	22
DOIs	https://doi.org/10.1093/bioinformatics/bti678
Publication status	Published - 15 Nov 2005
Externally published	Yes

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10.1093/bioinformatics/bti678

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title = "BADASP: Predicting functional specificity in protein families using ancestral sequences",

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 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.",

author = "Edwards, {Richard J.} and Shields, {Denis C.}",

note = "Funding Information: The authors would like to thank Dr Kate Johnston for suggestions during the preparation of the manuscript. This work was funded by the Health Research Board, Science Foundation Ireland and the Programme for Research in Third Level Institutions administered by the Higher Education Authority.",

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AU - Shields, Denis C.

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Y1 - 2005/11/15

N2 - 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.

AB - 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.

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BADASP: Predicting functional specificity in protein families using ancestral sequences

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