{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T08:30:00Z","timestamp":1772526600167,"version":"3.50.1"},"reference-count":38,"publisher":"Walter de Gruyter GmbH","issue":"3","license":[{"start":{"date-parts":[[2017,8,10]],"date-time":"2017-08-10T00:00:00Z","timestamp":1502323200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,8,10]]},"abstract":"Abstract<\/jats:title>Background<\/jats:italic><\/jats:title> Miniature inverted repeat transposable element (MITE) is a short transposable element, carrying no protein-coding regions. However, its high proliferation rate and sequence-specific insertion preference renders it as a good genetic tool for both natural evolution and experimental insertion mutagenesis. Recently active MITE copies are those with clear signals of Terminal Inverted Repeats (TIRs) and Direct Repeats (DRs), and are recently translocated into their current sites. Their proliferation ability renders them good candidates for the investigation of genomic evolution.<\/jats:p><\/jats:sec>Results<\/jats:italic><\/jats:title> This study optimizes the C++ code and running pipeline of the MITE Uncovering SysTem (MUST) by assuming no prior knowledge of MITEs required from the users, and the current version, MUSTv2, shows significantly increased detection accuracy for recently active MITEs, compared with similar programs. The running speed is also significantly increased compared with MUSTv1. We prepared a benchmark dataset, the simulated genome with 150 MITE copies for researchers who may be of interest.<\/jats:p><\/jats:sec>Conclusions<\/jats:italic><\/jats:title> MUSTv2 represents an accurate detection program of recently active MITE copies, which is complementary to the existing template-based MITE mapping programs. We believe that the release of MUSTv2 will greatly facilitate the genome annotation and structural analysis of the bioOMIC big data researchers.<\/jats:p><\/jats:sec>","DOI":"10.1515\/jib-2017-0029","type":"journal-article","created":{"date-parts":[[2017,8,10]],"date-time":"2017-08-10T10:01:44Z","timestamp":1502359304000},"source":"Crossref","is-referenced-by-count":16,"title":["MUSTv2: An Improved De Novo Detection Program for Recently Active Miniature Inverted Repeat Transposable Elements (MITEs)"],"prefix":"10.1515","volume":"14","author":[{"given":"Ruiquan","family":"Ge","sequence":"first","affiliation":[{"name":"School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, Zhejiang 310018, China"}]},{"given":"Guoqin","family":"Mai","sequence":"additional","affiliation":[{"name":"Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China"}]},{"given":"Ruochi","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China"}]},{"given":"Xundong","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, Zhejiang 310018, China"}]},{"given":"Qing","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, Zhejiang 310018, China"}]},{"given":"Fengfeng","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China"}]}],"member":"374","reference":[{"key":"ref371","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","article-title":"An efficient algorithm for large-scale detection of protein families","volume":"30","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1016\/j.bbrc.2007.11.038","article-title":"Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria","volume":"365","year":"2008","journal-title":"Biochem Biophys Res Commun"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"14651","DOI":"10.1038\/ncomms14651","article-title":"Translational repression by a miniature inverted-repeat transposable element in the 3\u2032 untranslated region","volume":"8","year":"2017","journal-title":"Nat Commun"},{"key":"ref331","doi-asserted-by":"crossref","first-page":"3659","DOI":"10.1093\/nar\/gkg531","article-title":"MAK, a computational tool kit for 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