Ortholog identification in the presence of domain architecture rearrangement

By Kimmen Sjölander, Ruchira S. Datta, Yaoqing Shen, Grant M. Shoffner. 2011

39 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

Uniclust databases of clustered and deeply annotated protein sequences and alignments (2016, background): “A high minimum overlap ensures that all proteins within one cluster have the same or a very similar domain structure and is also an effective criterion to achieve functional homogeneity (15).”
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, background): “Relationships between more rootward OGs and their nested children OGs at more specific taxonomic levels were explicitly tracked and ascertained to be consistent, with exceptions only for mosic proteins with multi-domain combinations, where individual domains might have evolved independently (26,27).”