User Manual

detectMITE User Manual

Table of Contents

1. What is detectMITE?
2. How to cite detectMITE?
3. How to install detectMITE?
4. How to run detectMITE?
5. Parameters for detectMITE
6. Outputs of detectMITE
7. Update history

1. What is detectMITE?

detectMITE is a MATLAB-based tool for detecting miniature inverted repeat transposable elements (MITEs) from genomes. This software is an open-source tool that follows specifications on website (http://creativecommons.org/licenses/by-nc-sa/3.0/).
If you have any question or comment, please contact with Dr. Chun Liang (liangc@miamioh.edu).

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2. How to cite detectMITE?

[1]. Ye C, Ji G, Liang C (2016) detectMITE: A novel approach to detect miniature inverted repeattransposable elements in genomes. Sci. Rep. 6, 19688
[2]. Ye C, Ji G, Li L, Liang C (2014) detectIR: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation. PLoS ONE 9(11): e113349.

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3. How to install detectMITE?

[1]. 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.

[2]. Download and install 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

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4. How to run detectMITE?

[1]. To run detectMITE, you shoule make sure the MATLAB environment is installed.
[2]. After opening the MATLAB, change the MATLAB's Working Path to the path where detectMITE is installed (e.g., './detectMITE').
[3]. Type the following command in the Command Window of MATLAB:

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

However, we also provide an example script 'Test_Demo.m' for using in the source code, all your need is to modify few values of the parameters in the script, and then run it.

[4]. Alternatively, you can run the program in background by typing the following command at the Linux prompt (you aslo should change the Working Path to the path where detectMITE is installed):

$ nohup matlab < Test_Demo.m > output.txt &

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5. Parameters for detectMITE

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;

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6. Outputs of detectMITE

[1]. MITE representative sequences of each family are placed in the file 'genome_name.mite.fasta' in the folder './detectMITE'.
The description line of each representative sequence (e.g., chr06|2367817|2367964|10|2|109) has the following explanation:
>ChromosomeName|GenomicStartPosition|GenomicStopPosition|TIR_Length|TSD_Length|CopyNumber.

Please notice that the TIR length is computed with at most 1 tolerated mismatch. The actual TIR length may be longer than the specified with looser limitations.

[2]. MITE families are placed in the file 'genome_name.miteSet.fasta' in the folder './detectMITE'. And each family are seperated by dot line.
The description line of each MITE sequence (e.g., >chr06|2367817|2367964|10|2) has the following explanation:
>ChromosomeName|GenomicStartPosition|GenomicStopPosition|TIR_Length|TSD_Length.

[3]. Files in the folder './detectMITE/result/' are temporary files generated during the program running, they could be deleted.

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7. Update history

To see the details of update history, go to https://sourceforge.net/p/detectmite/wiki/UpdateHistory/

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Project Members:

• Congting Ye (admin)
• liangc_mu (admin)