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 jbd/agilent/ file to make mcc use the system versions of various libraries rather than the versions that come with matlab.

Running JBD

If you're trying to run JBD from the command line without using the scripts that creates, you'll probably need to set your LD_LIBRARY_PATH to include
  • the jbd/agilent directory (the one in which you compiled JBD)
  • bin/glnx86 or bin/glnxa64 in your matlab distribution

Running TAMO

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 MATLAB library.
Contact Us
Computational Genomics Research Group, the Fraenkel Lab, and the Young Lab.