Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human.

ABSTRACT: Accurate predictions of orthology and paralogy relationships are necessary to infer human molecular function from experiments in model organisms. Previous genome-scale approaches to predicting these relationships have been limited by their use of protein similarity and their failure to take into account multiple splicing events and gene prediction errors. We have developed PhyOP, a new phylogenetic orthology prediction pipeline based on synonymous rate estimates, which accurately predicts orthology and paralogy relationships for transcripts, genes, exons, or genomic segments between closely related genomes. We were able to identify orthologue relationships to human genes for 93% of all dog genes from Ensembl. Among 1:1 orthologues, the alignments covered a median of 97.4% of protein sequen

SUBMITTER: Goodstadt L 

PROVIDER: S-EPMC1584324 | biostudies-literature | 2006 Sep

REPOSITORIES: biostudies-literature