DRIM Examples

Once you have installed the DRIM software, you can train using it with the following examples:


DNA Sequences Example

The following example shows CBF1 transcription factor binding motifs. Data is taken from:
Harbison, C. T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104 (2004).

Download the input file and save it in the same directory of DRIM, under the name "sequence_file_CBF1.txt".

Open a command prompt, change the path to DRIM's directory and write the following command:

  perl drim.pl -i sequence_file_CBF1.txt -l 6 -s Results_summary_CBF1.txt -f Full_results_CBF1.txt

At the end of the calculation you are supposed to get the following results files:

To visualize the motifs occurrences, open the Motif Discovery Visualization Tool (click here for instructions), and set the parameters as appear in the following picture:



Dataset path: select "sequence_file_CBF1.txt"
Dataset type: DNA
Paste the 'CACGTG' motif in the text box.
Number of top sequences to plot: 500

Click 'Plot' and you are supposed to get the following output window:




RNA Sequences Example

The following example is taken from Baek, D. et al. The impact of microRNAs on protein output. Nature 455, 64-71 (2008) and shows the enriched 7-nucleotide motifs of miR-124.

Download the input file and save it in the same directory of DRIM, under the name "sequence_file_miR-124.txt".

Open a command prompt, change the path to DRIM's directory and write the following command:

  perl drim.pl -i sequence_file_miR-124.txt -rna -l 7 -s Results_summary_miR-124.txt -f Full_results_miR-124.txt

As in the DNA example, you should get two results files, similar to the following ones:

To visualize the motifs occurrences, open the Motif Discovery Visualization Tool (click here for instructions), and set the parameters as appear in the following picture:



Dataset path: select "sequence_file_CBF1.txt"
Dataset type: DNA
Paste the 'CACGTG' motif in the text box.
Number of top sequences to plot: 500

Click 'Plot' and you are supposed to get the following output window:




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