Joint Binding Deconvolution
Downloading and Compiling JBD
You will need a recent version of Matlab to compile
JBD. While you can run JBD directly in Matlab, you'll want a compiled
version for most purposes.
If you're having trouble with the compiler, make sure you have a recent
version. We've used version 2006a with good results, but various 6.x
versions don't work. Also, you may need to modify the
- Download the JBD code
- Download the TAMO code
- Untar the JBD code. You will need to add some
subdirectories in the jbd directory to your matlab path. See the
as an example
- Compile JBD. From the
jbd/agilent directory, run
file to make mcc use the system versions of various libraries rather than the versions that
come with matlab.
If you're trying to run JBD from the command line without using the scripts that ep_cmdline.pl creates, you'll probably need to set your LD_LIBRARY_PATH to include
jbd/agilent directory (the one in which you compiled JBD)
bin/glnxa64 in your matlab distribution
The TAMO package
takes the positional priors and input sequences from JBD to run motif
discovery. See the Fraenkel Lab
pages for instructions on setting it up.
JBD uses the Lightspeed
Computational Genomics Research
Group, the Fraenkel Lab, and
the Young Lab.