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Hieranoid: Hierarchical Orthology Inference
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). Swedish E Sci Res Ctr, Stockholm, Sweden.
2013 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 425, no 11, 2072-2081 p.Article in journal (Refereed) Published
Abstract [en]

An accurate inference of orthologs is essential in many research fields such as comparative genomics, molecular evolution, and genome annotation. Existing methods for genome-scale orthology inference are mostly based on all-versus-all similarity searches that scale quadratically with the number of species. This limits their application to the increasing number of available large-scale datasets. Here, we present Hieranoid, a new orthology inference method using a hierarchical approach. Hieranoid performs pairwise orthology analysis using In Paranoid at each node in a guide tree as it progresses from its leaves to the root. This concept reduces the total runtime complexity from a quadratic to a linear function of the number of species. The tree hierarchy provides a natural structure in multi-species ortholog groups, and the aggregation of multiple sequences allows for multiple alignment similarity searching techniques, which can yield more accurate ortholog groups. Using the recently published orthobench benchmark, Hieranoid showed the overall best performance. Our progressive approach presents a new way to infer orthologs that combines efficient graph-based methodology with aspects of compute-intensive tree-based methods. The linear scaling with the number of species is a major advantage for large-scale applications and makes Hieranoid well suited to cope with vast amounts of sequenced genomes in the future. Hieranoid is an open source and can be downloaded at

Place, publisher, year, edition, pages
2013. Vol. 425, no 11, 2072-2081 p.
Keyword [en]
Orthology inference, inParanoid, guide tree, profile-profile comparison
National Category
Biochemistry and Molecular Biology
URN: urn:nbn:se:su:diva-92006DOI: 10.1016/j.jmb.2013.02.018ISI: 000320419300016OAI: diva2:637550
The Wenner-Gren Foundation


Available from: 2013-07-19 Created: 2013-07-15 Last updated: 2013-07-19Bibliographically approved

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Sonnhammer, Erik L. L.
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