Author

Alfonso E. Romero, Tamás Nepusz, Rajkumar Sasidharan, Alberto Paccanaro

This is the documentation of consat, a Python-based application to provide protein families defined as consensus domain architectures. consat is the stand-alone tool used in the homonym web server (http://www.paccanarolab.org/consat).

This tool takes a file of protein sequences, a file with domain assignments in InterProScan format, and a file with a library of HMMs domains not included in InterPro, and produces an assignment of proteins to protein families, as well as functional information association (mainly GO terms) based in those families.

As this software is an evolution of gfam (and also includes it), most of the changes have been propagated backwards, and this gives the possibility of running gfam with the new developments implemented in consat as well as with improvements in the original algorithm.

You will need the following tools to run consat:

• Python 2.7 (2.6 should work, but this is not 100% guaranteed).
• HMMer 3.0 (or newer versions).
• NCBI BLAST; if you are using gfam from this software package.

The latest release of SciPy is recommended, but not necessary. gfam uses SciPy for calculating the logarithm of the gamma function in the overrepresentation analysis routines, but it falls back to a (somewhat slower) Python implementation if SciPy is not installed.

consat is driven by a master configuration file named consat.cfg. A sample configuration file is given in the distribution. The sample file works fine for the gene sequences of Arabidopsis thaliana; for other species, you might have to tweak some of the parameters, and you will surely have to modify the paths to the data files and maybe other parameters. The configuration file is documented and mostly self-explanatory.

You can launch consat by typing:

$ bin/consat

This will run the whole consat analysis pipeline using the configuration specified in consat.cfg. If your configuration file is named otherwise, you can run it by typing:

$ bin/consat -c my_config.cfg

If you have a question or a comment about consat or you think you have found a bug, feel free to contact me.