MTGIpick is a software developed intending to identify Genomic Islands. For this purpose, it performs a robust multi-scale statistical strategy:

IST-LFS： an iteration of small-scale t-test with large-scale feature selection to quantifying the compositional difference between a region and the ’native’ genome regions.

MSA： a multiscale segmentation algorithm to investigate the variability of genomic signals and to identify large, multi-window segments.

CG-MJSD: An boundary detection method based on CG-based segmentation and Markovian Jensen–Shannon divergence.

SOFTWARE

1. Requirements

MTGIpick has been compiled and tested under Sun Java interpreter and Matlab. MTGIpick can be used in Windows- and Linux- platforms. Java Virtual Machine and MATLAB Compiler Runtime (MCR) are required for MTGIpick setup on your platform. However, we strongly advise the use of openjdk (JDK) instead of the Oracle version of java virtual machine when working in linux-based machines as the Oracle version may result in some exceptions during the analyses.

2. Download

1) You can download the MTGIpick Source code from our web ( http://bioinfo.zstu.edu.cn/MTGI )

Source code	Source code

There are two ways to download the MTGIpick:

2) You can download the MTGIpick package with JDK and MCR from our web ( http://bioinfo.zstu.edu.cn/MTGI )

Platform	Windows	Linux
MTGIpick (with JDK and MCR)	MTGIpick 1.2.0	MTGIpick 1.2.0
MTGIpick (without JDK or MCR)	MTGIpick 1.2.0	MTGIpick 1.2.0

3) If you download the MTGIpick package without 1.8 or MCR 8.4 (8.1) from our webs (http://bioinfo.zstu.edu.cn/MTGI, https://github.com/bioinfo0706/MTGIpick), download the JDK and MCR for your platform from the following Web:

JDK 1.8 : http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html#jdk-8u102-oth-JPR

MCR: http://www.mathworks.com/products/compiler/mcr/?refresh=true

Notice: Make sure that the JDK and MCR are saved into the folder of the MTGIpick, and please rename the MCR as MCRInstaller.

3. Install and Run

(1) Window (Tested on win7 X64)

Before installing MTGIpick, make sure that the MCR 8.4 for windows is saved into the same folder of MTGIpick software. Install MCR 8.4 first, and run MTGIpick setup directly.

(2) Linux (Tested on CentOS7)

Before installing MTGIpick, make sure that the JDK 1.8 (jdk-8u102-linux-x64.tar.gz) and MCR 8.1 for Linux are saved into the same folder of MTGIpick software. Please follow the following steps for installing and running MTGIpick:

Step 1: To install JDK 1.8 (jdk-8u102-linux-x64.tar.gz) and MCR 8.1, it requires a simple command line as follow:

> bash install_jdk-mcr_linux.sh

Step 2: To run the MTGIpick software, just type a simple command line as follow (Once the first step has run, execute the second step to run MTGIpick):

>bash run_MTGI_linux.sh

Click Documentation for detailed information.

Please cite: Qi Dai, Chaohui Bao, Yabing Hai, Sheng Ma, Tao Zhou, Cong Wang, Yunfei Wang, Xiaoqing Liu, Yuhua Yao, Wenwen Huo, Zhenyu Xuan, Min Chen and Michael Q Zhang. MTGIpick allows the robust identification of genomic islands from a single genome. To be submitted to Briefings in Bioinformatics.