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

• Published in: Bioinformatics (Oxford, England) England), 2016-08, Vol.32 (16), p.2502-2504
• Main Authors: Lee, Hyungro, Lee, Minsu, Mohammed Ismail, Wazim, Rho, Mina, Fox, Geoffrey C, Oh, Sangyoon, Tang, Haixu
• Format: Article
• Language: English
• Subjects: Algorithms; Computational Biology - methods; Genome; Programming Languages; Retroelements; Software; Systems Integration
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btw157

: 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× 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. MGEScan tutorials and source code are available at http://mgescan.readthedocs.org/ [e-mail] or [e-mail] Supplementary data are available at Bioinformatics online.