Full metadata record
DC Field | Value | Language |
---|---|---|
dc.contributor.author | 노미나 | - |
dc.date.accessioned | 2018-03-19T04:54:47Z | - |
dc.date.available | 2018-03-19T04:54:47Z | - |
dc.date.issued | 2016-04 | - |
dc.identifier.citation | BIOINFORMATICS, v. 32, NO 16, Page. 2502-2504 | en_US |
dc.identifier.issn | 1367-4803 | - |
dc.identifier.issn | 1460-2059 | - |
dc.identifier.uri | https://academic.oup.com/bioinformatics/article/32/16/2502/1743013 | - |
dc.identifier.uri | http://hdl.handle.net/20.500.11754/48867 | - |
dc.description.abstract | 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 3.26x 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. | en_US |
dc.description.sponsorship | This work was supported by National Research Foundation of Korea grants funded by the Ministry of Education (NRF-2015R1D1A1A01059557), by the Korean government (MSIP) (KW-2014PPD0053 and NRF-2015R1C1A1A01054305), by the National Science Foundation grant (DBI-1262588) and by Marine Biotechnology Program (PJT200620) of Ministry of Oceans and Fisheries. | en_US |
dc.language.iso | en | en_US |
dc.publisher | OXFORD UNIV PRESS | en_US |
dc.subject | TRANSPOSABLE ELEMENTS | en_US |
dc.subject | DAPHNIA-PULEX | en_US |
dc.title | MGEScan: a Galaxy-based system for identifying retrotransposons in genomes | en_US |
dc.type | Article | en_US |
dc.relation.no | 16 | - |
dc.relation.volume | 32 | - |
dc.identifier.doi | 10.1093/bioinformatics/btw157 | - |
dc.relation.page | 2502-2504 | - |
dc.relation.journal | BIOINFORMATICS | - |
dc.contributor.googleauthor | Lee, Hyungro | - |
dc.contributor.googleauthor | Lee, Minsu | - |
dc.contributor.googleauthor | Ismail, Wazim Mohammed | - |
dc.contributor.googleauthor | Rho, Mina | - |
dc.contributor.googleauthor | Fox, Geoffrey C. | - |
dc.contributor.googleauthor | Oh, Sangyoon | - |
dc.contributor.googleauthor | Tang, Haixu | - |
dc.relation.code | 2016001067 | - |
dc.sector.campus | S | - |
dc.sector.daehak | COLLEGE OF ENGINEERING[S] | - |
dc.sector.department | DEPARTMENT OF COMPUTER SCIENCE | - |
dc.identifier.pid | minarho | - |
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