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Bioinformatics Advance Access originally published online on November 14, 2006
Bioinformatics 2007 23(2):245-246; doi:10.1093/bioinformatics/btl566
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Detecting protein dissimilarities in multiple alignments using Bayesian variable selection

Sinae Kim , Jerry Tsai 1, Ioannis Kagiampakis 1, Patricia LiWang 1 and Marina Vannucci 2,*

Department of Biostatistics, University of Michigan Ann Arbor, MI, USA
1 Department of Biochemistry and Biophysics, Texas A&M University College Station, TX, USA
2 Department of Statistics, Texas A&M University College Station, TX, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: We present an application of Bayesian variable selection to the novel detection of sequence elements that confer negative design to protein structure and function. As an illustration, we analyze the different dimer interfaces between the CXCL8 chemokine family with the CCL4 and CCL2 chemokine families to discover the changes that disfavor CXCL8 of quaternary structure.

Results: In comparison with known experimental results, our method identifies evolutionarily conserved sequence changes in the CC families that inhibit CXCL8 quaternary structure. Therefore, we find positive selection of negative design elements. Furthermore, our approach predicts that a two-residue deletion conserved in the CCL4 chemokine family disfavors CXCL8 dimerization.

Availability: The Matlab code for the Bayesian variable selection is freely available at http://stat.tamu.edu/~mvannucci/webpages/codes.html

Contact: mvannucci{at}stat.tamu.edu

Associate Editor: Martin Bishop

Received on August 22, 2006; revised on November 6, 2006; accepted on November 7, 2006

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