The quest for orthologs: finding the corresponding gene across genomes

A. Kuzniar, R.C.H.J. van Ham, S. Pongor, J.A.M. Leunissen

Research output: Contribution to journalArticleAcademicpeer-review

174 Citations (Scopus)


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.
Original languageEnglish
Pages (from-to)539-551
JournalTrends in Genetics
Issue number11
Publication statusPublished - 2008


  • phylogenetic trees
  • network propagation
  • eukaryotic genomes
  • protein families
  • database
  • evolutionary
  • classification
  • life
  • phylogenomics
  • inference

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    Kuzniar, A., van Ham, R. C. H. J., Pongor, S., & Leunissen, J. A. M. (2008). The quest for orthologs: finding the corresponding gene across genomes. Trends in Genetics, 24(11), 539-551.