Open Source Software
Congenomics LLC provides four open source programs; Bio::FdrFet, Bio::SDRS, Congen, and SEEBUGS.
Bio::FdrFet is a Perl module for Gene Set Enrichment Analysis developed by Ruiru Ji, Karl-Heinz Ott, Roumyana Yordanova, and Robert E Bruccoleri. It uses the Fisher Exact Test to evaluate sets of disregulated genes in a pathway while scanning over different possible False Discovery Rates (FDR) looking for the FDR cutoff that yields the highest significance for a pathway. The module also contains an executable script along with a preprint of a paper on the method.
Bio::SDRS implements the Sigmoidal Dose Response Search of assay responses described in the paper by Rui-Ru Ji et al.
CONGEN is a general purpose molecular modeling program, which is especially designed to search the conformational space of loops and predict their structure. It is well suited for comparative modeling building as well as binding energy calculations. Please see the copyright notice page to get to the FTP site. A PDF version of the manual is also available.
SEEBUGS (Software for the Examination, Exploration, and Broad Understanding of Genome Sequences) is an effort to develop a tool for finding similar sequences across genomes. It is an exceptionally powerful tool for identifying essential genes in microbes. A paper describing SEEBUGS has appeared in Nucleic Acids Research 26, 4482-4486. The source code and database files can be obtained by contacting us.
These programs are provided without any warranty or support.