{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T09:13:16Z","timestamp":1762506796625},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,11,10]],"date-time":"2016-11-10T00:00:00Z","timestamp":1478736000000},"content-version":"vor","delay-in-days":183,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Simple Sequence Repeats (SSRs) are used to address a variety of research questions in a variety of fields (e.g. population genetics, phylogenetics, forensics, etc.), due to their high mutability within and between species. Here, we present an innovative algorithm, SA-SSR, based on suffix and longest common prefix arrays for efficiently detecting SSRs in large sets of sequences. Existing SSR detection applications are hampered by one or more limitations (i.e. speed, accuracy, ease-of-use, etc.). Our algorithm addresses these challenges while being the most comprehensive and correct SSR detection software available. SA-SSR is 100% accurate and detected &amp;gt;1000 more SSRs than the second best algorithm, while offering greater control to the user than any existing software.<\/jats:p>\n               <jats:p>Availability and implementation: SA-SSR is freely available at http:\/\/github.com\/ridgelab\/SA-SSR<\/jats:p>\n               <jats:p>Contact: \u00a0perry.ridge@byu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw298","type":"journal-article","created":{"date-parts":[[2016,5,12]],"date-time":"2016-05-12T03:15:00Z","timestamp":1463022900000},"page":"2707-2709","source":"Crossref","is-referenced-by-count":15,"title":["SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences"],"prefix":"10.1093","volume":"32","author":[{"given":"B. D.","family":"Pickett","sequence":"first","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT 84602, USA"}]},{"given":"S. M.","family":"Karlinsey","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT 84602, USA"}]},{"given":"C. E.","family":"Penrod","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT 84602, USA"}]},{"given":"M. J.","family":"Cormier","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT 84602, USA"}]},{"given":"M. T. W.","family":"Ebbert","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT 84602, USA"}]},{"given":"D. K.","family":"Shiozawa","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT 84602, USA"}]},{"given":"C. J.","family":"Whipple","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT 84602, USA"}]},{"given":"P. G.","family":"Ridge","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT 84602, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,5,11]]},"reference":[{"key":"2023020112593878100_btw298-B1","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/S1570-8667(03)00065-0","article-title":"Replacing suffix trees with enhanced suffix arrays","volume":"2","author":"Abouelhoda","year":"2004","journal-title":"J. Discrete Algorithms"},{"key":"2023020112593878100_btw298-B2","doi-asserted-by":"crossref","first-page":"1149","DOI":"10.1002\/(SICI)1097-024X(199911)29:13<1149::AID-SPE274>3.0.CO;2-O","article-title":"Reducing the space requirement of suffix trees","volume":"29","author":"Kurtz","year":"1999","journal-title":"Softw. Pract. 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