{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T03:07:44Z","timestamp":1774494464216,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2017,8,30]],"date-time":"2017-08-30T00:00:00Z","timestamp":1504051200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006756","name":"Brigham Young University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006756","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>One of the main challenges with bioinformatics software is that the size and complexity of datasets necessitate trading speed for accuracy, or completeness. To combat this problem of computational complexity, a plethora of heuristic algorithms have arisen that report a \u2018good enough\u2019 solution to biological questions. However, in instances such as Simple Sequence Repeats (SSRs), a \u2018good enough\u2019 solution may not accurately portray results in population genetics, phylogenetics and forensics, which require accurate SSRs to calculate intra- and inter-species interactions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present Kmer-SSR, which finds all SSRs faster than most heuristic SSR identification algorithms in a parallelized, easy-to-use manner. The exhaustive Kmer-SSR option has 100% precision and 100% recall and accurately identifies every SSR of any specified length. To identify more biologically pertinent SSRs, we also developed several filters that allow users to easily view a subset of SSRs based on user input. Kmer-SSR, coupled with the filter options, accurately and intuitively identifies SSRs quickly and in a more user-friendly manner than any other SSR identification algorithm.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code is freely available on GitHub at https:\/\/github.com\/ridgelab\/Kmer-SSR.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx538","type":"journal-article","created":{"date-parts":[[2017,8,29]],"date-time":"2017-08-29T19:12:16Z","timestamp":1504033936000},"page":"3922-3928","source":"Crossref","is-referenced-by-count":30,"title":["Kmer-SSR: a fast and exhaustive SSR search algorithm"],"prefix":"10.1093","volume":"33","author":[{"given":"Brandon D","family":"Pickett","sequence":"first","affiliation":[{"name":"Department of Biology, BYU, Provo, UT, USA"}]},{"given":"Justin B","family":"Miller","sequence":"additional","affiliation":[{"name":"Department of Biology, BYU, Provo, UT, USA"}]},{"given":"Perry G","family":"Ridge","sequence":"additional","affiliation":[{"name":"Department of Biology, BYU, Provo, UT, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,8,30]]},"reference":[{"key":"2023020207012322300_btx538-B1","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":"2023020207012322300_btx538-B2","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1093\/bioinformatics\/btt310","article-title":"Informed and automated k-mer size selection for genome assembly","volume":"30","author":"Chikhi","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020207012322300_btx538-B3","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/0004-3702(85)90016-5","article-title":"Heuristic classification","volume":"27","author":"Clancey","year":"1985","journal-title":"Artif. 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