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Ortholog identification in the presence of domain architecture rearrangement
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 m...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178056/ https://www.ncbi.nlm.nih.gov/pubmed/21712343 http://dx.doi.org/10.1093/bib/bbr036 |
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author | Sjölander, Kimmen Datta, Ruchira S. Shen, Yaoqing Shoffner, Grant M. |
author_facet | Sjölander, Kimmen Datta, Ruchira S. Shen, Yaoqing Shoffner, Grant M. |
author_sort | Sjölander, Kimmen |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3178056 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-31780562011-09-22 Ortholog identification in the presence of domain architecture rearrangement Sjölander, Kimmen Datta, Ruchira S. Shen, Yaoqing Shoffner, Grant M. Brief Bioinform Special Issue Papers 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. Oxford University Press 2011-09 2011-06-28 /pmc/articles/PMC3178056/ /pubmed/21712343 http://dx.doi.org/10.1093/bib/bbr036 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Special Issue Papers Sjölander, Kimmen Datta, Ruchira S. Shen, Yaoqing Shoffner, Grant M. Ortholog identification in the presence of domain architecture rearrangement |
title | Ortholog identification in the presence of domain architecture rearrangement |
title_full | Ortholog identification in the presence of domain architecture rearrangement |
title_fullStr | Ortholog identification in the presence of domain architecture rearrangement |
title_full_unstemmed | Ortholog identification in the presence of domain architecture rearrangement |
title_short | Ortholog identification in the presence of domain architecture rearrangement |
title_sort | ortholog identification in the presence of domain architecture rearrangement |
topic | Special Issue Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178056/ https://www.ncbi.nlm.nih.gov/pubmed/21712343 http://dx.doi.org/10.1093/bib/bbr036 |
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