{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:56Z","timestamp":1772138096111,"version":"3.50.1"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2019,7,9]],"date-time":"2019-07-09T00:00:00Z","timestamp":1562630400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100008569","name":"Oklahoma Center for the Advancement of Science and Technology","doi-asserted-by":"publisher","award":["PS17-015"],"award-info":[{"award-number":["PS17-015"]}],"id":[{"id":"10.13039\/100008569","id-type":"DOI","asserted-by":"publisher"}]},{"name":"College of Engineering and Natural Sciences"},{"name":"Tulsa Undergraduate Research Challenge Program"},{"DOI":"10.13039\/100007147","name":"University of Tulsa","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007147","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Simple tandem repeats, microsatellites in particular, have regulatory functions, links to several diseases and applications in biotechnology. There is an immediate need for an accurate tool for detecting microsatellites in newly sequenced genomes. The current available tools are either sensitive or specific but not both; some tools require adjusting parameters manually.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose Look4TRs, the first application of self-supervised hidden Markov models to discovering microsatellites. Look4TRs adapts itself to the input genomes, balancing high sensitivity and low false positive rate. It auto-calibrates itself. We evaluated Look4TRs on 26 eukaryotic genomes. Based on F measure, which combines sensitivity and false positive rate, Look4TRs outperformed TRF and MISA\u2014the most widely used tools\u2014by 78 and 84%. Look4TRs outperformed the second and the third best tools, MsDetector and Tantan, by 17 and 34%. On eight bacterial genomes, Look4TRs outperformed the second and the third best tools by 27 and 137%.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/TulsaBioinformaticsToolsmith\/Look4TRs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz551","type":"journal-article","created":{"date-parts":[[2019,7,8]],"date-time":"2019-07-08T23:11:44Z","timestamp":1562627504000},"page":"380-387","source":"Crossref","is-referenced-by-count":9,"title":["Look4TRs: a\n                    <i>de novo<\/i>\n                    tool for detecting simple tandem repeats using self-supervised hidden Markov models"],"prefix":"10.1093","volume":"36","author":[{"suffix":"II","given":"Alfredo","family":"Velasco","sequence":"first","affiliation":[{"name":"Bioinformatics Toolsmith Laboratory, Tandy School of Computer Science, University of Tulsa The , Tulsa, OK 74104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benjamin T","family":"James","sequence":"additional","affiliation":[{"name":"Bioinformatics Toolsmith Laboratory, Tandy School of Computer Science, University of Tulsa The , Tulsa, OK 74104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent D","family":"Wells","sequence":"additional","affiliation":[{"name":"Bioinformatics Toolsmith Laboratory, Tandy School of Computer Science, University of Tulsa The , Tulsa, OK 74104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hani Z","family":"Girgis","sequence":"additional","affiliation":[{"name":"Bioinformatics Toolsmith Laboratory, Tandy School of Computer Science, University of Tulsa The , Tulsa, OK 74104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,7,9]]},"reference":[{"key":"2023013112065026800_btz551-B1","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1093\/bioinformatics\/btl519","article-title":"Repseek, a tool to retrieve approximate repeats from large DNA sequences","volume":"23","author":"Achaz","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013112065026800_btz551-B2","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1093\/bioinformatics\/btx721","article-title":"PERF: an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large DNA sequences","volume":"34","author":"Avvaru","year":"2018","journal-title":"Bioinformatics"},{"key":"2023013112065026800_btz551-B3","doi-asserted-by":"crossref","first-page":"2583","DOI":"10.1093\/bioinformatics\/btx198","article-title":"MISA-web: a web server for microsatellite prediction","volume":"33","author":"Beier","year":"2017","journal-title":"Bioinformatics"},{"key":"2023013112065026800_btz551-B4","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: a program to analyze DNA sequences","volume":"27","author":"Benson","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2023013112065026800_btz551-B5","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1093\/bioinformatics\/btk032","article-title":"Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression","volume":"22","author":"Boeva","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013112065026800_btz551-B6","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/ng0497-327","article-title":"Big, bad minisatellites","volume":"15","author":"Buard","year":"1997","journal-title":"Nat. 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