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MGEScan: a Galaxy-based system for identifying retrotransposons in genomes
- MGEScan: a Galaxy-based system for identifying retrotransposons in genomes
- Lee, Hyungro; Lee, Minsu; Ismail, Wazim Mohammed; Rho, Mina; Fox, Geoffrey C.; Oh, Sangyoon; Tang, Haixu
- Ewha Authors
- SCOPUS Author ID
- Issue Date
- Journal Title
- 1367-4803; 1460-2059
- vol. 32, no. 16, pp. 2502 - 2504
- OXFORD UNIV PRESS
- SCI; SCIE; SCOPUS
- 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.
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