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.

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Cited by papers we hold 12

• OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity · 2022
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• OrthoDB in 2020: evolutionary and functional annotations of orthologs · 2020
  No notice
• OrthoFinder: phylogenetic orthology inference for comparative genomics · 2019
  No notice
• OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs · 2018
  No notice
• panX: pan-genome analysis and exploration · 2017
  No notice
• Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales · 2015
  No notice
• eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences · 2015
  No notice
• OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy · 2015
  No notice
• OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software · 2014
  No notice
• Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary · 2014
  No notice
• Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs · 2013
  No notice
• Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer · 2012
  No notice

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