%0 Journal Article %1 10.1371/journal.pcbi.1000262 %A Altenhoff, Adrian M. %A Dessimoz, Christophe %D 2009 %I Public Library of Science %J PLoS Comput Biol %K computational-biology genomics orthology %N 1 %P e1000262 %R 10.1371/journal.pcbi.1000262 %T Phylogenetic and Functional Assessment of Orthologs Inference %U http://dx.doi.org/10.1371%2Fjournal.pcbi.1000262 %V 5 %X <title>Author Summary</title> <p>The identification of orthologs, pairs of homologous genes in different species that started diverging through speciation events, is a central problem in genomics with applications in many research areas, including comparative genomics, phylogenetics, protein function annotation, and genome rearrangement. An increasing number of projects aim at inferring orthologs from complete genomes, but little is known about their relative accuracy or coverage. Because the exact evolutionary history of entire genomes remains largely unknown, predictions can only be validated indirectly, that is, in the context of the different applications of orthology. The few comparison studies published so far have asssessed orthology exclusively from the expectation that orthologs have conserved protein function. In the present work, we introduce methodology to verify orthology in terms of phylogeny and perform a comprehensive comparison of nine leading ortholog inference projects and two methods using both phylogenetic and functional tests. The results show large variations among the different projects in terms of performances, which indicates that the choice of orthology database can have a strong impact on any downstream analysis.</p>

@article{10.1371/journal.pcbi.1000262, abstract = { <title>Author Summary</title> <p>The identification of orthologs, pairs of homologous genes in different species that started diverging through speciation events, is a central problem in genomics with applications in many research areas, including comparative genomics, phylogenetics, protein function annotation, and genome rearrangement. An increasing number of projects aim at inferring orthologs from complete genomes, but little is known about their relative accuracy or coverage. Because the exact evolutionary history of entire genomes remains largely unknown, predictions can only be validated indirectly, that is, in the context of the different applications of orthology. The few comparison studies published so far have asssessed orthology exclusively from the expectation that orthologs have conserved protein function. In the present work, we introduce methodology to verify orthology in terms of phylogeny and perform a comprehensive comparison of nine leading ortholog inference projects and two methods using both phylogenetic and functional tests. The results show large variations among the different projects in terms of performances, which indicates that the choice of orthology database can have a strong impact on any downstream analysis.</p> }, added-at = {2010-01-02T19:38:14.000+0100}, author = {Altenhoff, Adrian M. and Dessimoz, Christophe}, biburl = {https://www.bibsonomy.org/bibtex/2ad26409dc3cec9477492a70a7c74a592/rwst}, doi = {10.1371/journal.pcbi.1000262}, interhash = {7db96afb8d8bc1b0d13985e73e8452f8}, intrahash = {ad26409dc3cec9477492a70a7c74a592}, journal = {PLoS Comput Biol}, keywords = {computational-biology genomics orthology}, month = {01}, number = 1, pages = {e1000262}, publisher = {Public Library of Science}, timestamp = {2010-01-02T19:38:14.000+0100}, title = {Phylogenetic and Functional Assessment of Orthologs Inference}, url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1000262}, volume = 5, year = 2009 }