TITLE

Ortholog identification in the presence of domain architecture rearrangement

AUTHOR(S)
Sjölander, Kimmen; Datta, Ruchira S.; Shen, Yaoqing; Shoffner, Grant M.
PUB. DATE
September 2011
SOURCE
Briefings in Bioinformatics;Sep2011, Vol. 12 Issue 5, p413
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Ortholog identification is used in gene functional annotation, species phylogeny estimation, phylogenetic profile construction and many other analyses. Bioinformatics methods for ortholog identification are commonly based on pairwise protein sequence comparisons between whole genomes. Phylogenetic methods of ortholog identification have also been developed; these methods can be applied to protein data sets sharing a common domain architecture or which share a single functional domain but differ outside this region of homology. While promiscuous domains represent a challenge to all orthology prediction methods, overall structural similarity is highly correlated with proximity in a phylogenetic tree, conferring a degree of robustness to phylogenetic methods. In this article, we review the issues involved in orthology prediction when data sets include sequences with structurally heterogeneous domain architectures, with particular attention to automated methods designed for high-throughput application, and present a case study to illustrate the challenges in this area.
ACCESSION #
66141637

 

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