Skip Navigation



MBE Advance Access published online on July 24, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl056
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/10/1937    most recent
msl056v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Gu, X.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Gu, X.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted July 6, 2006

Research Article

A Simple Statistical Method for Estimating Type-II (Cluster-Specific) Functional Divergence of Protein Sequences

Xun Gu 1 *

1 Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011

* To whom correspondence should be addressed.
Xun Gu, E-mail: xgu{at}iastate.edu


  Abstract

Predicting functional amino acid residues in silico is important for comparative genomics. In this paper, we focus on the issue of how to statistically identify cluster-specific amino acid residues that are related to the functional divergence after gene duplication. We approach this problem using a framework based on site-specific shift of amino acid property (type-II functional divergence), as opposed to site-specific shift of evolutionary rate (type-I functional divergence). An efficient statistical procedure is implemented to facilitate the development of phylogenomic database for cluster-specific residues of large-scale protein families. Our method has the following features: (1) statistical testing of the type-II functional divergence; and (2) the site-specific Bayesian profile to measure how amino acid residues contribute to type-II (cluster-specific) functional divergence. Consequently, one may obtain the posterior probability for ‘functional’ cluster-specific residues. Case-studies are presented and indicated that radical cluster-specific residues are responsible for most of inferred type-II functional divergence, while conserved cluster-specific residues appear less than even those imperfect radical cluster-specific residues to this type of functional divergence.

Keywords: Gene duplication; functional divergence.
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Plant Physiol.Home page
N. Georgelis, J. R. Shaw, and L. C. Hannah
Phylogenetic Analysis of ADP-Glucose Pyrophosphorylase Subunits Reveals a Role of Subunit Interfaces in the Allosteric Properties of the Enzyme
Plant Physiology, September 1, 2009; 151(1): 67 - 77.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
I. King Jordan, K. C. Kota, G. Cui, C. H. Thompson, and N. A. McCarty
Evolutionary and functional divergence between the cystic fibrosis transmembrane conductance regulator and related ATP-binding cassette transporters
PNAS, December 2, 2008; 105(48): 18865 - 18870.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
V. J. Lynch, A. Tanzer, Y. Wang, F. C. Leung, B. Gellersen, D. Emera, and G. P. Wagner
Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals
PNAS, September 30, 2008; 105(39): 14928 - 14933.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
C. Hernandez-Sanchez, A. Mansilla, F. de Pablo, and R. Zardoya
Evolution of the Insulin Receptor Family and Receptor Isoform Expression in Vertebrates
Mol. Biol. Evol., June 1, 2008; 25(6): 1043 - 1053.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
P. Courville, E. Urbankova, C. Rensing, R. Chaloupka, M. Quick, and M. F. M. Cellier
Solute Carrier 11 Cation Symport Requires Distinct Residues in Transmembrane Helices 1 and 6
J. Biol. Chem., April 11, 2008; 283(15): 9651 - 9658.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K. Ye, G. Vriend, and A. P. IJzerman
Tracing evolutionary pressure
Bioinformatics, April 1, 2008; 24(7): 908 - 915.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
T. Matsuo
Rapid Evolution of Two Odorant-Binding Protein Genes, Obp57d and Obp57e, in the Drosophila melanogaster Species Group
Genetics, February 1, 2008; 178(2): 1061 - 1072.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K. Ye, K. Anton Feenstra, J. Heringa, A. P. IJzerman, and E. Marchiori
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting
Bioinformatics, January 1, 2008; 24(1): 18 - 25.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.