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OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Author Rossier Victor, Warwick Vesztrocy Alex, Robinson-Rechavi Marc, Dessimoz Christophe,
Project Efficient and accurate comparative genomics to make sense of high volume low quality data in biology
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Original article (peer-reviewed)

Journal Bioinformatics
Page(s) btab219
Title of proceedings Bioinformatics
DOI 10.1093/bioinformatics/btab219

Open Access

Type of Open Access Publisher (Gold Open Access)


AbstractMotivationAssigning new sequences to known protein families and subfamilies is a prerequisite for many functional, comparative and evolutionary genomics analyses. Such assignment is commonly achieved by looking for the closest sequence in a reference database, using a method such as BLAST. However, ignoring the gene phylogeny can be misleading because a query sequence does not necessarily belong to the same subfamily as its closest sequence. For example, a hemoglobin which branched out prior to the hemoglobin alpha/beta duplication could be closest to a hemoglobin alpha or beta sequence, whereas it is neither. To overcome this problem, phylogeny-driven tools have emerged but rely on gene trees, whose inference is computationally expensive.ResultsHere, we first show that in multiple animal and plant datasets, 18–62% of assignments by closest sequence are misassigned, typically to an over-specific subfamily. Then, we introduce OMAmer, a novel alignment-free protein subfamily assignment method, which limits over-specific subfamily assignments and is suited to phylogenomic databases with thousands of genomes. OMAmer is based on an innovative method using evolutionarily informed k-mers for alignment-free mapping to ancestral protein subfamilies. Whilst able to reject non-homologous family-level assignments, we show that OMAmer provides better and quicker subfamily-level assignments than approaches relying on the closest sequence, whether inferred exactly by Smith-Waterman or by the fast heuristic DIAMOND.Availabilityand implementationOMAmer is available from the Python Package Index (as omamer), with the source code and a precomputed database available at informationSupplementary data are available at Bioinformatics online.