Literature DB >> 11934757

DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family.

Xun Gu1, Kent Vander Velden.   

Abstract

SUMMARY: DetectIng Variability in Evolutionary Rates among GEnes (DIVERGE) is a software system to study functional divergence of a protein family by detecting site-specific change in evolutionary rate using a multiple alignment of amino acid sequences for a given phylogenetic tree. The program first conducts a statistical test for site-specific rate shifts along the tree, and predicting candidate amino acid residues responsible for functional divergence based on posterior analysis. These results can then be mapped on the 3D protein structure if available. AVAILABILITY: DIVERGE is available free of charge from http://xgu1.zool.iastate.edu/. Distribution packages for both Linux and Microsoft Windows operating systems are available, including manual and example files.

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Year:  2002        PMID： 11934757     DOI： 10.1093/bioinformatics/18.3.500

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  128 in total

1.  Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information.

Authors:  Christian Blouin; Yan Boucher; Andrew J Roger
Journal:  Nucleic Acids Res       Date:  2003-01-15       Impact factor: 16.971

2.  Using evolutionary rates to investigate protein functional divergence and conservation. A case study of the carbonic anhydrases.

Authors:  Bjarne Knudsen; Michael M Miyamoto; Philip J Laipis; David N Silverman
Journal:  Genetics       Date:  2003-08       Impact factor: 4.562

3.  Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms.

Authors:  Andrew F Neuwald
Journal:  Stat Appl Genet Mol Biol       Date:  2011-08-04

4.  Molecular selection and functional divergence of HIF-α proteins in vertebrates.

Authors:  Xiangzhe Zhang; Minghui Wang; Guifang Tan; Qishan Wang; Hongbo Zhao; Yuchun Pan
Journal:  Genetica       Date:  2010-12-03       Impact factor: 1.082

5.  A Comprehensive Study of Molecular Evolution at the Self-Incompatibility Locus of Rosaceae.

Authors:  Jahanshah Ashkani; D J G Rees
Journal:  J Mol Evol       Date:  2015-12-29       Impact factor: 2.395

6.  Molecular evolution of ldpA, a gene mediating the circadian input signal in cyanobacteria.

Authors:  Volodymyr Dvornyk
Journal:  J Mol Evol       Date:  2005-01       Impact factor: 2.395

7.  Molecular phylogeny, evolution, and functional divergence of the LSD1-like gene family: inference from the rice genome.

Authors:  Qingpo Liu; Qingzhong Xue
Journal:  J Mol Evol       Date:  2007-01-16       Impact factor: 2.395

8.  Antarctic fish mitochondrial genomes lack ND6 gene.

Authors:  Chiara Papetti; Pietro Liò; Lukas Rüber; Tomaso Patarnello; Rafael Zardoya
Journal:  J Mol Evol       Date:  2007-10-23       Impact factor: 2.395

9.  Evolutionary analysis for functional divergence of the toll-like receptor gene family and altered functional constraints.

Authors:  Huaijun Zhou; Jianying Gu; Susan J Lamont; Xun Gu
Journal:  J Mol Evol       Date:  2007-08       Impact factor: 2.395

10.  Sequential duplications of an ancient member of the DnaJ-family expanded the functional chaperone network in the eukaryotic cytosol.

Authors:  Chandan Sahi; Jacek Kominek; Thomas Ziegelhoffer; Hyun Young Yu; Maciej Baranowski; Jaroslaw Marszalek; Elizabeth A Craig
Journal:  Mol Biol Evol       Date:  2013-01-16       Impact factor: 16.240
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