A probabilistic approach for de novo identification and classification of mobile genetic elements in eukaryotic genomes.

The following are required for installing and running MGEScan. The version numbers specified are the versions used for testing the latest release. Versions other than these may work but not guaranteed to give the same results. MGEScan is tested in Linux environment (Red Hat Enterprise Linux Server release 6.10 - Santiago). There has been issues reported in running the program in a Mac OS. Before proceeding to installation, please make sure that the binaries for the following software are available in $PATH by running the commands given below.

• git v2.0.0

git --version

• python v2.7.13

python --version

• virtualenv v15.1.0

virtualenv --version

• perl v5.10.1

perl --version

• HMMER v3.1b1

hmmsearch -h

• EMBOSS v6.6.0

transeq --version

• Tandem Repeats Finder v4.07b

trf --version

• NCBI BLAST+ v2.2.28

blastn -version

• Open MPI v2.1.0 (If you intend to use the MPI feature of MGEScan) - Note: Make sure that Open MPI binaries are available in $PATH.

mpicc --version

• Galaxy v17.01 (If you intend to use Galaxy platform to run MGEScan)
• RepeatMasker v4.0.5 (If you indend to use RepeatMasker in the preprocessing step of MGEScan-LTR)

Make sure the required prerequisites (see above) are all installed and their binaries are available in command-line by adding their paths to $PATH environment variable.

export MGESCAN_HOME=$HOME/mgescan4
export MGESCAN_VENV=$HOME/venv/mgescan

Note: Instead of the paths specified above, you can provide your own paths where you would like to install MGEScan and the Python virtual environment for MGEScan.

export GALAXY_HOME=$HOME/galaxy

Note: Replace the above path with the path where you've installed Galaxy.

virtualenv $MGESCAN_VENV
source $MGESCAN_VENV/bin/activate

git clone https://github.com/COL-IU/mgescan.git
cd mgescan
python setup.py install

Important: Check the following before running MGEScan

1. Make sure the environment variables (mentioned above) are exported every time before you run MGEScan. You can add the export commands in $HOME/.bash_profile (for bash shell) to have them automatically exported during login.
2. Make sure the Python virtual environment for MGEScan is activated every time before you run MGEScan.

source $MGESCAN_VENV/bin/activate

Usage:
    mgescan all <genome_dir> [--output=<data_dir>] [--mpi=<num>]
    mgescan ltr <genome_dir> [--output=<data_dir>] [--mpi=<num>]
    mgescan nonltr <genome_dir> [--output=<data_dir>] [--mpi=<num>]
    mgescan dna <genome_dir> [--output=<data_dir>] [--mpi=<num>]
    mgescan (-h | --help)
    mgescan --version

(To do)

How to cite MGEScan on Galaxy [here]

1. H. Lee, M. Lee, W. M. Ismail, M. Rho, G. C. Fox, S. Oh, H. Tang (2016), MGEScan: a Galaxy-based system for identifying retrotransposons in genomes, Bioinformatics, 32(16): 2502-2504.

2. M. Rho, S. Schaack, X. Gao, S. Kim, M. Lynch and H. Tang (2010), LTR retroelements in the genome of Daphnia pulex, BMC Genomics, 11:425. Pubmed.

3. M. Rho and H. Tang (2009), MGEScan-nonLTR: computational identification and classification of Non-LTR retrotransposons in eukaryotic genomes. Nucleic Acid Res, 37(21):e143. Free fulltext at NAR online

4. M. Rho, J. H. Choi, S. Kim, M. Lynch and H. Tang (2007), De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics, 8:90. Pubmed.

• MGEScan-LTR
• MGEScan-nonLTR

Copyright (C) 2015. See the LICENSE file for license rights and limitations (GPL v3).

This program is part of MGEScan.

MGEScan is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.