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APPLES Updates

11/09/2012: More Working Examples and Documentation

We have added some more working examples to the VM image, and uploaded some more documentation to

The virtual machine image and source code have been updated and are now available from

For reference, the old versions can still be downloaded:

15/08/2012: Motif Scoring Example

We have provided an updated version of the APPLES modules which perform motif scoring. You can install these inside the VM using the following commands:

wget && sh

This patch gets the file and installs a new version of empirical_scoringREV830 inside the VM.

After installing the patch, you may examine the script ~/VM/motifs/ Running this script will reproduce motif scoring and overrepresentation results using some freely available motifs on the conserved non-coding sequences (CNS) in the promoter of Arabidopsis gene AT1G01030. The results of the script are written to ~/VM/motifs/real_binomial.

NOTE: Running this script for the first time will take a long time (we left it running for around 10 hours) since it needs to compute profiles for all motifs and store them in the cache database. Running the script a second time for a different set of CNS will be much faster.