The quest for orthologs: finding the corresponding gene across genomes
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...
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| Published in | Trends in genetics Vol. 24; no. 11; pp. 539 - 551 |
|---|---|
| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
Amsterdam
Elsevier Ltd
01.11.2008
Cambridge, UK: Elsevier Trends Journals Elsevier |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0168-9525 |
| DOI | 10.1016/j.tig.2008.08.009 |
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| Abstract | 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. |
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| AbstractList | 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. 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.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. |
| Author | van Ham, Roeland C.H.J. Leunissen, Jack A.M. Pongor, Sándor Kuzniar, Arnold |
| Author_xml | – sequence: 1 givenname: Arnold surname: Kuzniar fullname: Kuzniar, Arnold organization: Laboratory of Bioinformatics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands – sequence: 2 givenname: Roeland C.H.J. surname: van Ham fullname: van Ham, Roeland C.H.J. organization: Laboratory of Bioinformatics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands – sequence: 3 givenname: Sándor surname: Pongor fullname: Pongor, Sándor organization: Protein Structure and Bioinformatics, International Centre for Genetic Engineering and Biotechnology, AREA Science Park, Padriciano 99, 34012 Trieste, Italy – sequence: 4 givenname: Jack A.M. surname: Leunissen fullname: Leunissen, Jack A.M. email: jack.leunissen@wur.nl organization: Laboratory of Bioinformatics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=20860160$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/18819722$$D View this record in MEDLINE/PubMed |
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| SubjectTerms | 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 |
| Title | The quest for orthologs: finding the corresponding gene across genomes |
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