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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 http://www.wsbc.warwick.ac.uk/peterkrusche/APPLES/docs/.

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

http://www.wsbc.warwick.ac.uk/peterkrusche/APPLES/APPLESVM-1.0.ova

http://www.wsbc.warwick.ac.uk/peterkrusche/APPLES/APPLES_11092012.zip

For reference, the old versions can still be downloaded:

http://www.wsbc.warwick.ac.uk/peterkrusche/APPLES/APPLESVM.zip

http://www.wsbc.warwick.ac.uk/peterkrusche/APPLES/APPLES.zip


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:

cd
wget http://www.wsbc.warwick.ac.uk/peterkrusche/APPLES/get_update.sh && sh get_update.sh

This patch gets the file http://www.wsbc.warwick.ac.uk/peterkrusche/APPLES/patch_motifs.tar.gz and installs a new version of empirical_scoringREV830 inside the VM.

After installing the patch, you may examine the script ~/VM/motifs/test_motif_overrepresentation.pl. 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.