DRIM Manual



Install and Run DRIM on Windows

DRIM requires having Perl on your computer. To download and install Perl click here or visit Perl.org.

Once you have downloaded DRIM, unrar and extract it to any location on your computer (It is recommended to place DRIM in your data directory).
In order to run DRIM, open a command line and go to the correct path. Use the following command:

  perl drim.pl -i <Input File> [other options]...


DRIM Input

The input to DRIM is an ordered list of DNA or RNA sequences. There are two acceptable formats:

(!) DRIM can handle sequences up to 2000bp. In case of longer sequences, DRIM cuts them and uses the first 2000bp only.


DRIM Parameters

DRIM has a variety of running options using flags. Some of the options can also be defined in a parameter file.

General parameters:

Parameters that control the exhaustive motif space search:

Advanced Parameters:


DRIM Results

DRIM has three output files:
The Seed motifs list, which displays all the seed motifs that passed the significance threshold, before the post processing stage.
The Results summary and Full results files, which display only the motifs that had a significacne score after the post processing (expansion) stage.

The Results summary file:

A summary of the seed motifs and their expansions that passed the significance threshold and the similarity filtering.
It is recommended to open this file with Microsoft Excel (Results summary example).

Explanation for some of the output columns:

Most of the above columns appear twice - the first result is for the seed motif and the second for its expansion.

The full results file:

A more detailed output for each of the enriched motifs that went through the post processing stage. It includes the motifs occurrences and PSSM (Full results example).

The seed motifs list:

A list of all the seed motifs that passed the significance threshold before entering the post processing stage (Seed motifs example).


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For more information please contact: inbalos@tx.technion.ac.il