{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T16:03:48Z","timestamp":1761581028385},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1467,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Spoligotyping is a well-established genotyping technique based on the presence of unique DNA sequences in Mycobacterium tuberculosis (Mtb), the causal agent of tuberculosis disease (TB). Although advances in sequencing technologies are leading to whole-genome bacterial characterization, tens of thousands of isolates have been spoligotyped, giving a global view of Mtb strain diversity. To bridge the gap, we have developed SpolPred, a software to predict the spoligotype from raw sequence reads. Our approach is compared with experimentally and de novo assembly determined strain types in a set of 44 Mtb isolates. In silico and experimental results are identical for almost all isolates (39\/44). However, SpolPred detected five experimentally false spoligotypes and was more accurate and faster than the assembling strategy. Application of SpolPred to an additional seven isolates with no laboratory data led to types that clustered with identical experimental types in a phylogenetic analysis using single-nucleotide polymorphisms. Our results demonstrate the usefulness of the tool and its role in revealing experimental limitations.<\/jats:p>\n               <jats:p>Availability and implementation: SpolPred is written in C and is available from www.pathogenseq.org\/spolpred.<\/jats:p>\n               <jats:p>Contact: \u00a0francesc.coll@lshtm.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics Online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts544","type":"journal-article","created":{"date-parts":[[2012,9,27]],"date-time":"2012-09-27T15:51:08Z","timestamp":1348761068000},"page":"2991-2993","source":"Crossref","is-referenced-by-count":82,"title":["SpolPred: rapid and accurate prediction of <i>Mycobacterium tuberculosis<\/i> spoligotypes from short genomic sequences"],"prefix":"10.1093","volume":"28","author":[{"given":"Francesc","family":"Coll","sequence":"first","affiliation":[{"name":"1 Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton and 3Department of Computer Science and Information Systems, Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Birkbeck College, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kim","family":"Mallard","sequence":"additional","affiliation":[{"name":"1 Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton and 3Department of Computer Science and Information Systems, Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Birkbeck College, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark D.","family":"Preston","sequence":"additional","affiliation":[{"name":"1 Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton and 3Department of Computer Science and Information Systems, Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Birkbeck College, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephen","family":"Bentley","sequence":"additional","affiliation":[{"name":"1 Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton and 3Department of Computer Science and Information Systems, Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Birkbeck College, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julian","family":"Parkhill","sequence":"additional","affiliation":[{"name":"1 Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton and 3Department of Computer Science and Information Systems, Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Birkbeck College, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruth","family":"McNerney","sequence":"additional","affiliation":[{"name":"1 Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton and 3Department of Computer Science and Information Systems, Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Birkbeck College, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nigel","family":"Martin","sequence":"additional","affiliation":[{"name":"1 Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton and 3Department of Computer Science and Information Systems, Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Birkbeck College, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taane G.","family":"Clark","sequence":"additional","affiliation":[{"name":"1 Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton and 3Department of Computer Science and Information Systems, Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Birkbeck College, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,9,26]]},"reference":[{"key":"2023012513222760700_bts544-B1","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/1471-2334-11-110","article-title":"The use of 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Dis."},{"key":"2023012513222760700_bts544-B2","first-page":"216","article-title":"Spacer oligonucleotide typing of bacteria of the Mycobacterium tuberculosis complex: recommendations for standardised nomenclature","volume":"5","author":"Dale","year":"2001","journal-title":"Int. J. Tuber. Lung Dis."},{"key":"2023012513222760700_bts544-B3","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1016\/j.meegid.2012.02.004","article-title":"SITVITWEB\u2014a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology","volume":"12","author":"Demay","year":"2012","journal-title":"Infect. Genet. 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Microbiol."},{"key":"2023012513222760700_bts544-B5","doi-asserted-by":"crossref","first-page":"e7778","DOI":"10.1371\/journal.pone.0007778","article-title":"Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa","volume":"4","author":"Ioerger","year":"2009","journal-title":"PLoS One"},{"key":"2023012513222760700_bts544-B6","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1128\/jcm.35.4.907-914.1997","article-title":"Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology","volume":"35","author":"Kamerbeek","year":"1997","journal-title":"J. Clin. Microbiol."},{"key":"2023012513222760700_bts544-B7","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1046\/j.1365-2672.2003.01918.x","article-title":"Molecular methods for Mycobacterium tuberculosis strain typing: a users guide","volume":"94","author":"Kanduma","year":"2003","journal-title":"J. Appl. Microbiol."},{"key":"2023012513222760700_bts544-B8","doi-asserted-by":"crossref","first-page":"2393","DOI":"10.1128\/JB.182.9.2393-2401.2000","article-title":"Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria","volume":"182","author":"van Embden","year":"2000","journal-title":"J. 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