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MGEScan: a Galaxy-based system for identifying retrotransposons in genomes

Title
MGEScan: a Galaxy-based system for identifying retrotransposons in genomes
Authors
Lee, HyungroLee, MinsuIsmail, Wazim MohammedRho, MinaFox, Geoffrey C.Oh, SangyoonTang, Haixu
Ewha Authors
이민수
SCOPUS Author ID
이민수scopus
Issue Date
2016
Journal Title
BIOINFORMATICS
ISSN
1367-4803JCR Link1460-2059JCR Link
Citation
vol. 32, no. 16, pp. 2502 - 2504
Publisher
OXFORD UNIV PRESS
Indexed
SCI; SCIE; SCOPUS WOS scopus
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.
DOI
10.1093/bioinformatics/btw157
Appears in Collections:
엘텍공과대학 > 컴퓨터공학과 > Journal papers
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