GFam (or gfam) is a Python module to aid the automatic annotation of gene families based on consensus domain architectures. gfam started out as a collection of loosely coupled Python scripts that process the output of iprscan (a tool to obtain domain assignments of individual genes from InterPro) and conduct some analyses using BLAST to detect novel, previously uncharacterised domains. The original domains and the detected novel domain candidates are then used to create a consensus domain assignment for each gene sequence. Genes are then finally assigned to families based on their domain architectures. Finally, the tool derives functional labels for families based on the Gene Ontology and an assignment between InterPro domains and Gene Ontology terms. Optionally, a Gene Ontology overrepresentation analysis can also be conducted on the GO annotations of individual domains in the same sequence to reinforce the functional labels.
You will need the following tools to run gfam:
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.
gfam is driven by a master configuration file named gfam.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. The configuration file is documented and mostly self-explanatory.
If you do not have a configuration file for some reason, or you want to generate a new one from scratch, you can ask gfam to do it:
$ bin/gfam init
This will create a default configuration file named gfam.cfg (if it does not exist already) and lists the configuration options you have to set in the file before starting GFam.
If the configuration file is well in order, you can launch gfam by typing:
$ bin/gfam
This will run the whole gfam analysis pipeline using the configuration specified in gfam.cfg. If your configuration file is named otherwise, you can run it by typing:
$ bin/gfam -c my_config.cfg
The results will be put into whatever work directory you specified in the configuration file. By default, this is named work. See Output files for more details on what will be calculated and where you can find them.
If you have a question or a comment about gfam or you think you have found a bug, feel free to contact me using the email address given in the header of this document.