detectMITE Files

detectMITE - a MATLAB-based tool for detecting miniature inverted repeat transposable elements (MITEs) from genomes. 
If you have any question or comment, please contact with Dr. Chun Liang (liangc@miamioh.edu).

[1]. This software is an open-source tool that follows specifications on website (http://creativecommons.org/licenses/by-nc-sa/3.0/)


[2]. Download and unzip our source codes - 'detectMITE.20170425.tar.gz'

After you download and unzip our source codes ('detectMITE.20170425.tar.gz'), you will see a folder named detectMITE, where all source codes and relevant documents are located.


[3]. Software required by detectMITE

CD-HIT: http://weizhong-lab.ucsd.edu/cd-hit/
Download the source codes of cd-hit and put it in the folder of './detectMITE'. Then, install the cd-hit as follow,
	$ tar xvf cd-hit-v4.6.1-2012-08-27.tgz ./
	$ mv cd-hit-v4.6.1-2012-08-27 cd-hit
	$ cd ./cd-hit
	$ make
	$ cd ..
	$ mkdir result


[4]. How to run detectMITE

tic;do_MITE_detection(data_file,'-genome','rice');runtime = toc;

Necessary parameters:
data_file		-	The location of the genome file, for example, data_file =  './data/rice_genome.fasta'. The genome file should be in fasta format.

Optional parameters:
-tir_length		-	Define the minimum length of terminal inverted repeat (TIR), default value = 10.
-tsd_minimum_length	-	Define the minimum length of target site duplication (TSD), default value = 2.
-tsd_maximum_length	-	Define the maximum length of TSD, default value = 10.
-mite_minimum_length	-	Define the minimum length of MITE, default value = 50.
-mite_maximum_length	-	Define the maximum length of MITE, default value = 800.
-genome			-	Define a name for the genome, default name = 'genome'.
-cpu			-	Number of CPU to be used, default number = 1;


[5]. Outputs

MITE representative sequences of each family are in the file 'genome_name.mite.fasta' in the folder './detectMITE'.
MITE families are in the file 'genome_name.miteSet.fasta' in the folder './detectMITE'. Each family are seperated by dashes.