GCFinder Software

GCFinder finds conserved gene clusters on multiple genomes based on constraining the overall size of a cluster that allows statistical significance estimates to be associated with each cluster. Two variants are provided:

• The first is a restricted version that can be solved in polynomial time which requires that a cluster appears in every input chromosome, none of the genes appear in more than one orthologous group and orthologous genes are strictly ordered within each cluster without allowing paralogous copies.
• The second is an exact algorithm for the unrestricted version that has exponential time complexity in the worst case which guarantees that all maximal unordered clusters with the lowest e-values are found.

Installing GCFinder

The GCFinder source code, including sample input and output files, can be compiled under the Unix/Linux/Windows(Cygwin) environment. The following steps will create a directory called gcfinder. Detailed usage of GCFinder is provided in a README file.

• gunzip gcfinder.tar.gz
• tar xvf gcfinder.tar
• cd gcfinder
• ./install

A list of maximal unordered gene clusters found on four bacterial genomes B. subtilis, S. pyogenes, S. pneumoniae and C. acetobutylicum, and four yeast genomes S. cerevisiae, S. paradoxus, S. mikatae and S. bayanus, is also included with the download. The maximum size of a gene cluster is constrained to be 50.

Examples

Below are gene clusters found on four bacterial genomes B. subtilis, S. pyogenes, S. pneumoniae and C. acetobutylicum:

• Top five clusters that appear in all the four genomes:
  • S10-spc-alpha superoperon with e-value 2.7e-131
  • prpC-prkC operon with e-value 3.6e-39
  • atp operon with e-value 1.7e-37
  • nusA-infB operon with e-value 1.7e-37
  • Oligopeptide ABC transporter system with e-value 1.2e-33
• Clusters that have many intervening genes:
  • ihk-irr system with e-value 1.5e-20
  • pur operon with e-value 2.1e-15
• Clusters in which some genes appear in two orthologous groups:
  • fru operon with e-value 8.6e-14
  • Glutamine ABC transporter system with e-value 8.6e-14

Below are gene clusters that appear in four yeast genomes S. cerevisiae, S. paradoxus, S. mikatae and S. bayanus:

• Top cluster with e-value 4.1e-95
• Cluster with e-value 4.4e-74

Please refer to the README file for an explanation of the output format.

Reference

Yang Q., Yi G., Zhang F., Thon M.R. and Sze S.-H. (2010) Identifying gene clusters within localized regions in multiple genomes. Journal of Computational Biology, 17, 657-668.