title: Orthology prediction methods: a quality assessment using curated protein families.
abstract: The increasing number of sequenced genomes has prompted the development of several automated orthology prediction methods. Tests to evaluate the accuracy of predictions and to explore biases caused by biological and technical factors are therefore required. We used 70 manually curated families to analyze the performance of five public methods in Metazoa. We analyzed the strengths and weaknesses of the methods and quantified the impact of biological and technical challenges. From the latter part of the analysis, genome annotation emerged as the largest single influencer, affecting up to 30% of the performance. Generally, most methods did well in assigning orthologous group but they failed to assign the exact number of genes for half of the groups. The publicly available benchmark set (http://eggnog.embl.de/orthobench/) should facilitate the improvement of current orthology assignment protocols, which is of utmost importance for many fields of biology and should be tackled by a broad scientific community.
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Kalliopi
authors.initials: K
authors.lastname: Trachana
authors.forename: Tomas A
authors.initials: TA
authors.lastname: Larsson
authors.forename: Sean
authors.initials: S
authors.lastname: Powell
authors.forename: Wei-Hua
authors.initials: WH
authors.lastname: Chen
authors.forename: Tobias
authors.initials: T
authors.lastname: Doerks
authors.forename: Jean
authors.initials: J
authors.lastname: Muller
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D030562:Databases, Protein; D005796:Genes; D020407:Internet; D058977:Molecular Sequence Annotation; D009077:Mucins / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D011506:Proteins / Q000235:genetics* / Q000378:metabolism; D015203:Reproducibility of Results; D013045:Species Specificity; D014584:User-Computer Interface
chemical_list: D009077:Mucins; D011506:Proteins