Ortholog identification in the presence of domain architecture rearrangement

Sjolander, K.; Datta, R. S.; Shen, Y.; Shoffner, G. M.

doi:10.1093/bib/bbr036

Ortholog identification in the presence of domain architecture rearrangement

Journal Article · Tue Jun 28 00:00:00 EDT 2011 · Briefings in Bioinformatics

DOI:https://doi.org/10.1093/bib/bbr036· OSTI ID:1904524

Sjolander, K. ^[1]; Datta, R. S. ^[2]; Shen, Y. ^[2]; Shoffner, G. M. ^[2]

University of California, Berkeley, CA (United States); Univ. of California, Berkeley, CA
University of California, Berkeley, CA (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: University of California, Berkeley, CA (United States); University of California, Oakland, CA (United States)

Sponsoring Organization:: National Science Foundation (NSF); USDOE Office of Science (SC)

Grant/Contract Number:: SC0004916

OSTI ID:: 1904524

Journal Information:: Briefings in Bioinformatics, Journal Name: Briefings in Bioinformatics Journal Issue: 5 Vol. 12; ISSN 1467-5463

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
97 MATHEMATICS AND COMPUTING
function prediction
multi-domain architecture
orthology
phylogenomics
promiscuous domains
super-ortholog

Ortholog identification in the presence of domain architecture rearrangement

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