MGEScan: a Galaxy-based system for identifying retrotransposons in genomes
- Title
- MGEScan: a Galaxy-based system for identifying retrotransposons in genomes
- Author
- 노미나
- Keywords
- TRANSPOSABLE ELEMENTS; DAPHNIA-PULEX
- Issue Date
- 2016-04
- Publisher
- OXFORD UNIV PRESS
- Citation
- BIOINFORMATICS, v. 32, NO 16, Page. 2502-2504
- 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.
- URI
- https://academic.oup.com/bioinformatics/article/32/16/2502/1743013http://hdl.handle.net/20.500.11754/48867
- ISSN
- 1367-4803; 1460-2059
- DOI
- 10.1093/bioinformatics/btw157
- Appears in Collections:
- COLLEGE OF ENGINEERING[S](공과대학) > COMPUTER SCIENCE(컴퓨터소프트웨어학부) > Articles
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