{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T08:55:59Z","timestamp":1769936159662,"version":"3.49.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: MGEScan-long terminal repeat (LTR) and MGEScan-non-LTR are successfully used programs for identifying LTRs and non-LTR retrotransposons in eukaryotic genome sequences. However, these programs are not supported by easy-to-use interfaces nor well suited for data visualization in general data formats. Here, we present MGEScan, a user-friendly system that combines these two programs with a Galaxy workflow system accelerated with MPI and Python threading on compute clusters. MGEScan and Galaxy empower researchers to identify transposable elements in a graphical user interface with ready-to-use workflows. MGEScan also visualizes the custom annotation tracks for mobile genetic elements in public genome browsers. A maximum speed-up of 3.26\u00d7 is attained for execution time using concurrent processing and MPI on four virtual cores. MGEScan provides four operational modes: as a command line tool, as a Galaxy Toolshed, on a Galaxy-based web server, and on a virtual cluster on the Amazon cloud.<\/jats:p>\n               <jats:p>Availability and implementation: MGEScan tutorials and source code are available at http:\/\/mgescan.readthedocs.org\/<\/jats:p>\n               <jats:p>Contact: \u00a0hatang@indiana.edu or syoh@ajou.ac.kr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw157","type":"journal-article","created":{"date-parts":[[2016,4,8]],"date-time":"2016-04-08T18:25:27Z","timestamp":1460139927000},"page":"2502-2504","source":"Crossref","is-referenced-by-count":27,"title":["MGEScan: a Galaxy-based system for identifying retrotransposons in genomes"],"prefix":"10.1093","volume":"32","author":[{"given":"Hyungro","family":"Lee","sequence":"first","affiliation":[{"name":"1 School of Informatics and Computing, Indiana University, Bloomington, IN, USA"}]},{"given":"Minsu","family":"Lee","sequence":"additional","affiliation":[{"name":"2 Department of Computer Science and Engineering, Ewha Womans University, Seoul, Korea"}]},{"given":"Wazim","family":"Mohammed Ismail","sequence":"additional","affiliation":[{"name":"1 School of Informatics and Computing, Indiana University, Bloomington, IN, USA"}]},{"given":"Mina","family":"Rho","sequence":"additional","affiliation":[{"name":"3 Department of Computer Science and Engineering, Hanyang University, Seoul, Korea"}]},{"given":"Geoffrey C.","family":"Fox","sequence":"additional","affiliation":[{"name":"1 School of Informatics and Computing, Indiana University, Bloomington, IN, USA"}]},{"given":"Sangyoon","family":"Oh","sequence":"additional","affiliation":[{"name":"4 Department of Software Convergence Technology, Ajou University, Suwon, Korea"}]},{"given":"Haixu","family":"Tang","sequence":"additional","affiliation":[{"name":"1 School of Informatics and Computing, Indiana University, Bloomington, IN, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,4,7]]},"reference":[{"key":"2023020112541339900_btw157-B1","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1126\/science.1197761","article-title":"The ecoresponsive genome of Daphnia pulex","volume":"331","author":"Colbourne","year":"2011","journal-title":"Science"},{"key":"2023020112541339900_btw157-B2","doi-asserted-by":"crossref","first-page":"w30","DOI":"10.1093\/nar\/gkv397","article-title":"HMMER web server: 2015 update","volume":"43","author":"Finn","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020112541339900_btw157-B3","doi-asserted-by":"crossref","first-page":"7704","DOI":"10.1073\/pnas.94.15.7704","article-title":"Transposable elements are sources of variation in animals and plants","volume":"94","author":"Kidwell","year":"1997","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020112541339900_btw157-B4","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"Lander","year":"2001","journal-title":"Nature"},{"key":"2023020112541339900_btw157-B5","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/1471-2164-8-90","article-title":"De novo identification of LTR retrotransposons in eukaryotic genomes","volume":"8","author":"Rho","year":"2007","journal-title":"BMC Genomics"},{"key":"2023020112541339900_btw157-B6","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1186\/1471-2164-11-425","article-title":"LTR retroelements in the genome of Daphnia pulex","volume":"11","author":"Rho","year":"2010","journal-title":"BMC Genomics"},{"key":"2023020112541339900_btw157-B7","doi-asserted-by":"crossref","first-page":"e143.","DOI":"10.1093\/nar\/gkp752","article-title":"MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes","volume":"37","author":"Rho","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023020112541339900_btw157-B8","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1038\/nrg2165","article-title":"A unified classification system for eukaryotic transposable elements","volume":"8","author":"Wicker","year":"2007","journal-title":"Nature Rev. Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/16\/2502\/49020670\/bioinformatics_32_16_2502.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/16\/2502\/49020670\/bioinformatics_32_16_2502.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:53:11Z","timestamp":1675291991000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/16\/2502\/1743013"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,4,7]]},"references-count":8,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2016,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw157","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,8,15]]},"published":{"date-parts":[[2016,4,7]]}}}