Computational Biology & Evolution

Archive for the ‘orthology’ tag

MetaPhOrs video tutorial (meta orthology prediction)

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Read more at the openHelix blog.

MetaPhOrs (Pryszcz, et al. 2010) is a public repository of phylogeny-based orthology and paralogy predictions that were computed using resources available in seven popular homology prediction services (PhylomeDB, EnsemblCompara, EggNOG, OrthoMCL, COG, Fungal Orthogroups, and TreeFam).

Written by jaime

June 1st, 2011 at 1:15 pm

Posted in Bioinformatics

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The pea aphid genome and phylome

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With the sequencing of the Acyrthosiphon pisum genome [1], aphid research enters the genome era. The reconstruction of the complete collection of evolutionary histories of aphid  genes and their homologues in other sequenced arthropods [2] has not only helped in the annotation of the genome sequence but has also already provided important insights into the evolution of this specialized hemipteran. In particular, we undertook a phylogenetic analysis for every protein of this species in a context 13 other fully-sequenced arthropods and three out-group species. Subsequent analyses have revealed multiple gene expansions that are specific to aphids and have served to transfer functional annotations to 4058 pea aphid genes that display one-to-one orthology relationships with Drosophila melanogaster annotated genes. To our knowledge, this is the first time that such a reliable methodology has been applied in the annotation pipeline of a newly sequenced genome.

  1. Genome sequence of the pea aphid Acyrthosiphon pisum. International Aphid Genomics Consortium. PLoS Biol. 2010 Feb 23;8(2):e1000313.
  2. The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes. J. Huerta-Cepas, M. Marcet-Houben, M. Pignatelli, A. Moya and T. Gabaldón

Written by jaime

March 17th, 2010 at 11:20 am