{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T20:17:51Z","timestamp":1792441071463,"version":"4.5.0"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,11,11]],"date-time":"2016-11-11T00:00:00Z","timestamp":1478822400000},"content-version":"vor","delay-in-days":822,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,10,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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.<\/jats:p>","DOI":"10.1093\/nar\/gku739","type":"journal-article","created":{"date-parts":[[2014,8,13]],"date-time":"2014-08-13T09:39:03Z","timestamp":1407922743000},"page":"e144-e144","source":"Crossref","is-referenced-by-count":385,"title":["COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification"],"prefix":"10.1093","volume":"42","author":[{"given":"Daniel","family":"Struck","sequence":"first","affiliation":[{"name":"1Laboratory of Retrovirology, CRP-Sant\u00e9, 84, Val Fleuri, L-1526, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9781-063X","authenticated-orcid":false,"given":"Glenn","family":"Lawyer","sequence":"additional","affiliation":[{"name":"2Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne-Marie","family":"Ternes","sequence":"additional","affiliation":[{"name":"1Laboratory of Retrovirology, CRP-Sant\u00e9, 84, Val Fleuri, L-1526, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Claude","family":"Schmit","sequence":"additional","affiliation":[{"name":"1Laboratory of Retrovirology, CRP-Sant\u00e9, 84, Val Fleuri, L-1526, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danielle Perez","family":"Bercoff","sequence":"additional","affiliation":[{"name":"1Laboratory of Retrovirology, CRP-Sant\u00e9, 84, Val Fleuri, L-1526, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,8,12]]},"reference":[{"key":"2026080306012651000_B1","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1126\/science.288.5463.55d","article-title":"HIV-1 nomenclature proposal","volume":"288","author":"Robertson","year":"2000","journal-title":"Science"},{"key":"2026080306012651000_B2","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1086\/314557","article-title":"Human immunodeficiency virus type 1 subtypes differ in disease progression","volume":"179","author":"Kanki","year":"1999","journal-title":"J. Infect. Dis."},{"key":"2026080306012651000_B3","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1086\/340130","article-title":"Effect of human immunodeficiency virus (HIV) type 1 envelope subtypes A and D on disease progression in a large cohort of HIV-1-positive persons in Uganda","volume":"185","author":"Kaleebu","year":"2002","journal-title":"J. Infect. Dis."},{"key":"2026080306012651000_B4","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1086\/527416","article-title":"Effect of human immunodeficiency virus Type 1 (HIV-1) subtype on disease progression in persons from Rakai, Uganda, with incident HIV-1 infection","volume":"197","author":"Kiwanuka","year":"2008","journal-title":"J. Infect. Dis."},{"key":"2026080306012651000_B5","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1086\/499952","article-title":"Different rates of disease progression of HIV type 1 infection in Tanzania based on infecting subtype","volume":"42","author":"Vasan","year":"2006","journal-title":"Clin. Infect. Dis."},{"key":"2026080306012651000_B6","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1086\/341833","article-title":"No difference in clinical progression between patients infected with the predominant human immunodeficiency virus type 1 circulating recombinant form (CRF) 02_AG strain and patients not infected with CRF02_AG, in Western and West-Central Africa: a four-year prospective multicenter study","volume":"186","author":"Laurent","year":"2002","journal-title":"J. Infect. Dis."},{"key":"2026080306012651000_B7","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1089\/aid.2005.21.221","article-title":"Impact of HIV type 1 genetic subtype on the outcome of antiretroviral therapy","volume":"21","author":"Atlas","year":"2005","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"2026080306012651000_B8","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.1086\/598502","article-title":"Effect of HIV-1 subtype on virologic and immunologic response to starting highly active antiretroviral therapy","volume":"48","author":"Geretti","year":"2009","journal-title":"Clin. Infect. Dis."},{"key":"2026080306012651000_B9","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1086\/342680","article-title":"Impact of human immunodeficiency virus type 1 subtypes on virologic response and emergence of drug resistance among children in the Paediatric European Network for Treatment of AIDS (PENTA) 5 trial","volume":"186","author":"Pillay","year":"2002","journal-title":"J. Infect. Dis."},{"key":"2026080306012651000_B10","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1128\/AAC.01668-12","article-title":"HIV-1 subtype is an independent predictor of reverse transcriptase mutation K65R in HIV-1 patients treated with combination antiretroviral therapy including tenofovir","volume":"57","author":"Theys","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"2026080306012651000_B11","doi-asserted-by":"crossref","first-page":"1590","DOI":"10.1056\/NEJMra0706737","article-title":"The challenge of HIV-1 subtype diversity","volume":"358","author":"Taylor","year":"2008","journal-title":"N. Engl. J. Med."},{"key":"2026080306012651000_B12","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1086\/521677","article-title":"Increasing prevalence of HIV-1 subtype A in Greece: estimating epidemic history and origin","volume":"196","author":"Paraskevis","year":"2007","journal-title":"J. Infect. Dis."},{"key":"2026080306012651000_B13","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1742-4690-10-7","article-title":"HIV-1 subtype distribution and its demographic determinants in newly diagnosed patients in Europe suggest highly compartmentalized epidemics","volume":"10","author":"Abecasis","year":"2013","journal-title":"Retrovirology"},{"key":"2026080306012651000_B14","doi-asserted-by":"crossref","first-page":"3896","DOI":"10.1128\/JCM.00515-08","article-title":"Reliability of rapid subtyping tools compared to that of phylogenetic analysis for characterization of human immunodeficiency virus type 1 non-B subtypes and recombinant forms","volume":"46","author":"Holgu\u00edn","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"2026080306012651000_B15","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.1097\/01.aids.0000237368.64488.ae","article-title":"Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity","volume":"20","author":"Gifford","year":"2006","journal-title":"AIDS"},{"key":"2026080306012651000_B16","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/1742-4690-7-25","article-title":"The role of recombination in the emergence of a complex and dynamic HIV epidemic","volume":"7","author":"Zhang","year":"2010","journal-title":"Retrovirology"},{"key":"2026080306012651000_B17","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1097\/QAD.0b013e328342ff93","article-title":"Global trends in molecular epidemiology of HIV-1 during 2000-2007","volume":"25","author":"Hemelaar","year":"2011","journal-title":"AIDS"},{"key":"2026080306012651000_B18","doi-asserted-by":"crossref","first-page":"3797","DOI":"10.1093\/bioinformatics\/bti607","article-title":"An automated genotyping system for analysis of HIV-1 and other microbial sequences","volume":"21","author":"de Oliveira","year":"2005","journal-title":"Bioinformatics"},{"key":"2026080306012651000_B19","doi-asserted-by":"crossref","first-page":"e1000581","DOI":"10.1371\/journal.pcbi.1000581","article-title":"An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1","volume":"5","author":"Kosakovsky Pond","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2026080306012651000_B20","doi-asserted-by":"crossref","first-page":"3535","DOI":"10.1093\/bioinformatics\/bti569","article-title":"A statistical model for HIV-1 sequence classification using the subtype analyser (STAR)","volume":"21","author":"Myers","year":"2005","journal-title":"Bioinformatics"},{"key":"2026080306012651000_B21","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1186\/1471-2105-7-265","article-title":"A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes","volume":"7","author":"Schultz","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2026080306012651000_B22","doi-asserted-by":"crossref","first-page":"e36566","DOI":"10.1371\/journal.pone.0036566","article-title":"Classification of HIV-1 sequences using profile Hidden Markov Models","volume":"7","author":"Dwivedi","year":"2012","journal-title":"PLoS ONE"},{"key":"2026080306012651000_B23","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1007\/978-1-61779-582-4_7","article-title":"Alignment methods: strategies, challenges, benchmarking, and comparative overview","volume":"855","author":"L\u00f6ytynoja","year":"2012","journal-title":"Methods Mol. Biol."},{"key":"2026080306012651000_B24","doi-asserted-by":"crossref","first-page":"7120","DOI":"10.1093\/nar\/gki1020","article-title":"Automatic assessment of alignment quality","volume":"33","author":"Lassmann","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2026080306012651000_B25","first-page":"216","article-title":"Sequence alignment in HIV computational analysis","volume-title":"HIV Sequence Compendium 2006\/2007. Theoretical Biology and Biophysics Group","author":"Abecasis","year":"2007"},{"key":"2026080306012651000_B26","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1093\/bioinformatics\/btg005","article-title":"Alignment-free sequence comparison-a review","volume":"19","author":"Vinga","year":"2003","journal-title":"Bioinformatics"},{"key":"2026080306012651000_B27","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.1109\/TIT.2005.844059","article-title":"Clustering by compression","volume":"51","author":"Cilibrasi","year":"2005","journal-title":"IEEE Trans. Inf. Theory"},{"key":"2026080306012651000_B28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-8-1","article-title":"Comparing sequences without using alignments: application to HIV\/SIV subtyping","volume":"8","author":"Didier","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2026080306012651000_B29","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1186\/1471-2105-11-406","article-title":"MS4\u2013Multi-Scale Selector of Sequence Signatures: an alignment-free method for classification of biological sequences","volume":"11","author":"Corel","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2026080306012651000_B30","doi-asserted-by":"crossref","first-page":"1416","DOI":"10.1093\/nar\/gks1285","article-title":"One size does not fit all: on how Markov model order dictates performance of genomic sequence analyses","volume":"41","author":"Narlikar","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2026080306012651000_B31","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1109\/TCOM.1984.1096090","article-title":"Data compression using adaptive coding and partial string matching","volume":"32","author":"Cleary","year":"1984","journal-title":"IEEE Trans. Commun."},{"key":"2026080306012651000_B32","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1613\/jair.1491","article-title":"On prediction using variable order Markov models","volume":"22","author":"Begleiter","year":"2004","journal-title":"J. Artif. Intell. Res."},{"key":"2026080306012651000_B33","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1186\/1471-2105-8-252","article-title":"Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment","volume":"8","author":"Ferragina","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2026080306012651000_B34","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.meegid.2013.04.032","article-title":"Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools","volume":"19","author":"Pineda-Pe\u00f1a","year":"2013","journal-title":"Infect. Genet. Evol."},{"key":"2026080306012651000_B35","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"2026080306012651000_B36","doi-asserted-by":"crossref","first-page":"W654","DOI":"10.1093\/nar\/gkh419","article-title":"A web-based genotyping resource for viral sequences","volume":"32","author":"Rozanov","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2026080306012651000_B37","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1002\/hep.26744","article-title":"Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment Web resource","volume":"59","author":"Smith","year":"2014","journal-title":"Hepatology"},{"key":"2026080306012651000_B38","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1093\/nar\/26.2.544","article-title":"Microbial gene identification using interpolated Markov models","volume":"26","author":"Salzberg","year":"1998","journal-title":"Nucleic Acids Res."},{"key":"2026080306012651000_B39","doi-asserted-by":"crossref","first-page":"5203","DOI":"10.1093\/nar\/gkl669","article-title":"Sequence determinants of breakpoint location during HIV-1 intersubtype recombination","volume":"34","author":"Baird","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2026080306012651000_B40","doi-asserted-by":"crossref","first-page":"e1000178","DOI":"10.1371\/journal.pcbi.1000178","article-title":"Identifying the important HIV-1 recombination breakpoints","volume":"4","author":"Archer","year":"2008","journal-title":"PLoS Comput. Biol."},{"key":"2026080306012651000_B41","doi-asserted-by":"crossref","first-page":"307","DOI":"10.2307\/1912557","article-title":"Likelihood ratio tests for model selection and non-nested hypotheses","volume":"57","author":"Vuong","year":"1989","journal-title":"Econometrica"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/42\/18\/e144\/70406477\/nar_42_18_e144.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/42\/18\/e144\/70406477\/nar_42_18_e144.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T10:01:38Z","timestamp":1785751298000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/42\/18\/e144\/2434545"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,8,12]]},"references-count":41,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2014,10,13]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gku739","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,10]]},"published":{"date-parts":[[2014,8,12]]}}}