{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T00:27:26Z","timestamp":1784334446204,"version":"3.55.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2017,10,18]],"date-time":"2017-10-18T00:00:00Z","timestamp":1508284800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31570534"],"award-info":[{"award-number":["31570534"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Microsatellites are found to be related with various diseases and widely used in population genetics as genetic markers. However, it remains a challenge to identify microsatellite from large genome and screen microsatellites for primer design from a huge result dataset. Here, we present Krait, a robust and flexible tool for fast investigation of microsatellites in DNA sequences. Krait is designed to identify all types of perfect or imperfect microsatellites on a whole genomic sequence, and is also applicable to identification of compound microsatellites. Primer3 was seamlessly integrated into Krait so that users can design primer for microsatellite amplification in an efficient way. Additionally, Krait can export microsatellite results in FASTA or GFF3 format for further analysis and generate statistical report as well as plotting.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Krait is freely available at https:\/\/github.com\/lmdu\/krait under GPL2 License, implemented in C and Python, and supported on Windows, Linux and Mac operating systems.<\/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\/btx665","type":"journal-article","created":{"date-parts":[[2017,10,17]],"date-time":"2017-10-17T11:10:08Z","timestamp":1508238608000},"page":"681-683","source":"Crossref","is-referenced-by-count":210,"title":["Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design"],"prefix":"10.1093","volume":"34","author":[{"given":"Lianming","family":"Du","sequence":"first","affiliation":[{"name":"Institute for Advanced Study, Chengdu University, Chengdu, Sichuan, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qin","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Life Sciences and Food Engineering, Yibin University, Yibin, Sichuan, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiuyue","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bisong","family":"Yue","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,10,18]]},"reference":[{"key":"2023012712384221900_btx665-B1","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1093\/jhered\/ess082","article-title":"MSDB: a user-friendly program for reporting distribution and building databases of microsatellites from genome sequences","volume":"104","author":"Du","year":"2013","journal-title":"J. Hered"},{"key":"2023012712384221900_btx665-B2","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1038\/nrg1348","article-title":"Microsatellites: simple sequences with complex evolution","volume":"5","author":"Ellegren","year":"2004","journal-title":"Nat. Rev. Genet"},{"key":"2023012712384221900_btx665-B3","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1111\/j.1471-8286.2007.01884.x","article-title":"msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design","volume":"8","author":"Faircloth","year":"2008","journal-title":"Mol. Ecol. Resour"},{"key":"2023012712384221900_btx665-B4","doi-asserted-by":"crossref","first-page":"2038","DOI":"10.1101\/gr.122937.111","article-title":"A matter of life or death: how microsatellites emerge in and vanish from the human genome","volume":"21","author":"Kelkar","year":"2011","journal-title":"Genome Res"},{"key":"2023012712384221900_btx665-B5","doi-asserted-by":"crossref","first-page":"1683","DOI":"10.1093\/bioinformatics\/btm157","article-title":"SciRoKo: a new tool for whole genome microsatellite search and investigation","volume":"23","author":"Kofler","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012712384221900_btx665-B6","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1093\/bib\/bbn028","article-title":"Detecting short tandem repeats from genome data: opening the software black box","volume":"9","author":"Merkel","year":"2008","journal-title":"Brief. Bioinform"},{"key":"2023012712384221900_btx665-B7","first-page":"R13","article-title":"Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions","volume":"4","author":"Subramanian","year":"2003","journal-title":"Genome Res"},{"key":"2023012712384221900_btx665-B8","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1007\/s00122-002-1031-0","article-title":"Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)","volume":"106","author":"Thiel","year":"2003","journal-title":"Theor. Appl. Genet"},{"key":"2023012712384221900_btx665-B9","doi-asserted-by":"crossref","first-page":"e115","DOI":"10.1093\/nar\/gks596","article-title":"Primer3\u2013new capabilities and interfaces","volume":"40","author":"Untergasser","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023012712384221900_btx665-B10","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1590\/1678-4685-GMB-2016-0027","article-title":"Microsatellite markers: what they mean and why they are so useful","volume":"39","author":"Vieira","year":"2016","journal-title":"Genet. Mol. Biol"},{"key":"2023012712384221900_btx665-B11","first-page":"1350","article-title":"GMATA: An Integrated software package for genome-scale SSR mining, marker development and viewing","volume":"7","author":"Wang","year":"2016","journal-title":"Front. Plant Sci"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/4\/681\/48913500\/bioinformatics_34_4_681.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/4\/681\/48913500\/bioinformatics_34_4_681.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:29:43Z","timestamp":1674826183000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/4\/681\/4557187"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,10,18]]},"references-count":11,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2018,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx665","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,2,15]]},"published":{"date-parts":[[2017,10,18]]}}}