title: COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification.
abstract: Viral sequence classification has wide applications in clinical, epidemiological, structural and functional categorization studies. Most existing approaches rely on an initial alignment step followed by classification based on phylogenetic or statistical algorithms. Here we present an ultrafast alignment-free subtyping tool for human immunodeficiency virus type one (HIV-1) adapted from Prediction by Partial Matching compression. This tool, named COMET, was compared to the widely used phylogeny-based REGA and SCUEAL tools using synthetic and clinical HIV data sets (1,090,698 and 10,625 sequences, respectively). COMET's sensitivity and specificity were comparable to or higher than the two other subtyping tools on both data sets for known subtypes. COMET also excelled in detecting and identifying new recombinant forms, a frequent feature of the HIV epidemic. Runtime comparisons showed that COMET was almost as fast as USEARCH. This study demonstrates the advantages of alignment-free classification of viral sequences, which feature high rates of variation, recombination and insertions/deletions. COMET is free to use via an online interface.
authors.affiliation: Laboratory of Retrovirology, CRP-Santé, 84, Val Fleuri, L-1526, Luxembourg daniel.struck@crp-sante.lu.
authors.forename: Daniel
authors.initials: D
authors.lastname: Struck
authors.affiliation: Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany.
authors.forename: Glenn
authors.identifier: http://orcid.org/0000-0001-9781-063X
authors.initials: G
authors.lastname: Lawyer
authors.affiliation: Laboratory of Retrovirology, CRP-Santé, 84, Val Fleuri, L-1526, Luxembourg.
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Ternes
authors.affiliation: Laboratory of Retrovirology, CRP-Santé, 84, Val Fleuri, L-1526, Luxembourg.
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Schmit
authors.affiliation: Laboratory of Retrovirology, CRP-Santé, 84, Val Fleuri, L-1526, Luxembourg.
authors.forename: Danielle Perez
authors.initials: DP
authors.lastname: Bercoff
mesh_terms: D000465:Algorithms; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D010802:Phylogeny; D012984:Software