Motif Independent Metric
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Failed to load latest commit information.


[MIM: Motif Independet Metric - Luca Pinello]

This software calculates a measure of sequence specificity called Motif Independent Metric. 


In order to use the MIM software you need:

-Python 2.7( 

and the following modules:

-Numpy (
-Scipy (

If you are using the Windows 64 bit version of Python, you must download the 64 bit version of the modules from:


The program takes as input:

1) A proper BED file ( containing the coordinates of your sequences for some reference genome

2) The fasta files of your reference genome (

To launch the program from a shell type:

python bed_file.bed /path_to_your_genome_directory/

To see a list of the optional arguments with a short explanation, please just type:


At the end of the execution the program will report the MIM value for the sequences extracted from the bed file and its p-value.


1) Download the human genome (hg18) fasta files from here:
and extract all the files from in a directory (for example hg18_directory).

2) Run the program with the following command:

python sample_hg18.bed hg18_directory

Notes: If you want to build a more realiable null model, you can use the parameter --null_rep to increase the sampling accuracy (the default value is 1000):

python sample_hg18.bed hg18_directory --null_rep 5000

You can also use a null model that shuffle the input sequences instead of random sampling sequence from genome with the optional parameter --null_model:

python sample_hg18.bed hg18_directory --null_model shuffle