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 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.
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.
Below are gene clusters found on four bacterial genomes B. subtilis, S. pyogenes, S. pneumoniae and C. acetobutylicum:
Below are gene clusters that appear in four yeast genomes S. cerevisiae, S. paradoxus, S. mikatae and S. bayanus:
Please refer to the README file for an explanation of the output format.
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.