GFam – Automatic annotation of gene families

This is the documentation of gfam, a Python module to aid the automatic annotation of gene families based on consensus domain architecture, written by Tamás Nepusz.

GFam has no official publication yet, but there will soon be one. You are kindly asked to cite the webpage of GFam until an official GFam publication comes out:

GFam: a platform for automatic annotation of gene families

Tamás Nepusz, Rajkumar Sasidharan, David Swarbreck, Eva Huala and

Alberto Paccanaro. <http://github.com/ntamas/gfam>

GFam can generally be considered stable. We have used it successfully to annotate the whole genome of Arabidopsis thaliana and Arabidopsis lyrata. Please email the author if you discover any bugs, or feel free to submit a bug report on GitHub.

If you are interested in the latest and greatest (but maybe unstable) version of GFam, you can get it from GitHub - just click on the Download source button on the GitHub page.

• Introduction
  • What is GFam?
  • Requirements
  • For the impatient
  • Questions, comments
• Running GFam
  • Input files
  • The configuration file
  • Output files
  • Command line options
• Steps of the GFam pipeline
  • Overview of a GFam analysis
  • Step 1 – Extracting valid gene IDs
  • Step 2 – Preliminary domain architecture
  • Step 3 – Finding unassigned sequence fragments
  • Step 4 – All-against-all BLAST comparison and filtering
  • Step 5 – Calculation of Jaccard similarity
  • Step 6 – Identification of novel domains
  • Step 7 – Consensus domain architecture
  • Step 8 – Functional label assignment
  • Step 9 – Overrepresentation analysis
• Supplementary scripts
  • Plotting descriptive statistics of the input file
  • Updating the mapping of IDs to human-readable names
• API documentation
  • gfam – The main module
  • gfam.assignment – Routines related to sequence-domain annotations
  • gfam.blast – Handling BLAST file formats and utilities
  • gfam.compat – Compatibility classes for Python 2.5
  • gfam.config – Configuration file handling
  • gfam.enum – A simple enumeration class
  • gfam.fasta – FASTA parser and emitter
  • gfam.go – Handling the Gene Ontology
  • gfam.interpro – Handling InterPro-related files
  • gfam.modula – Modular calculation framework
  • gfam.sequence – Simple sequence and sequence record classes
  • gfam.scripts – Command line scripts
  • gfam.utils – Utility classes and functions

Indices and tables

• Index
• Module Index
• Search Page