title: MGEScan: a Galaxy-based system for identifying retrotransposons in genomes.
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 3.26× 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/
  
  
  
  hatang@indiana.edu or syoh@ajou.ac.kr
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN, USA.
authors.forename: Hyungro
authors.initials: H
authors.lastname: Lee
authors.affiliation: Department of Computer Science and Engineering, Ewha Womans University, Seoul, Korea.
authors.forename: Minsu
authors.initials: M
authors.lastname: Lee
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN, USA.
authors.forename: Wazim
authors.initials: W
authors.lastname: Mohammed Ismail
authors.affiliation: Department of Computer Science and Engineering, Hanyang University, Seoul, Korea.
authors.forename: Mina
authors.initials: M
authors.lastname: Rho
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN, USA.
authors.forename: Geoffrey C
authors.initials: GC
authors.lastname: Fox
authors.affiliation: Department of Software Convergence Technology, Ajou University, Suwon, Korea.
authors.forename: Sangyoon
authors.initials: S
authors.lastname: Oh
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN, USA.
authors.forename: Haixu
authors.initials: H
authors.lastname: Tang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D016678:Genome; D011381:Programming Languages; D018626:Retroelements; D012984:Software; D018511:Systems Integration
chemical_list: D018626:Retroelements