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.
- 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
example
startup.m as an example
- Compile JBD. From the
jbd/agilent
directory, run make jbd
.
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/mbuildopts.sh
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 ep_cmdline.pl 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.