The quest for orthologs: finding the corresponding gene across genomes

• Published in: Trends in genetics Vol. 24; no. 11; pp. 539 - 551
• Main Authors: Kuzniar, Arnold, van Ham, Roeland C.H.J., Pongor, Sándor, Leunissen, Jack A.M.
• Format: Journal Article
• Language: English
• Published: Amsterdam Elsevier Ltd 01.11.2008; Cambridge, UK: Elsevier Trends Journals; Elsevier
• Subjects: Animals; bioinformatics; Biological and medical sciences; Biological evolution; classification; Databases, Genetic; eukaryotic genomes; Evolution, Molecular; evolutionary; Fundamental and applied biological sciences. Psychology; genes; Genetics of eukaryotes. Biological and molecular evolution; Genome; genomics; Genomics - methods; Humans; inference; life; Medical Education; Molecular and cellular biology; network propagation; phylogenetic trees; phylogenomics; Phylogeny; protein families; proteins; Proteins - chemistry; Sequence Homology; Molecular evolution; Gene; Molecular phylognetic; Orthologous gene; Genetics; Review; Method; Genome; Bioinformatics
• ISSN: 0168-9525
• DOI: 10.1016/j.tig.2008.08.009

Orthology is a key evolutionary concept in many areas of genomic research. It provides a framework for subjects as diverse as the evolution of genomes, gene functions, cellular networks and functional genome annotation. Although orthologous proteins usually perform equivalent functions in different species, establishing true orthologous relationships requires a phylogenetic approach, which combines both trees and graphs (networks) using reliable species phylogeny and available genomic data from more than two species, and an insight into the processes of molecular evolution. Here, we evaluate the available bioinformatics tools and provide a set of guidelines to aid researchers in choosing the most appropriate tool for any situation.