ModuleMaster is an advanced program for finding cis-regulatory modules. It is capable of retrieving sequences, performing matrix scans on these sequences and finally, searching for cis-regulatory modules. It offers a huge list of options and features to customize it for your needs. Everything can be automated. The program offers an easy-to-use GUI, job-processing and command-line capabilities.

ModuleMaster is able to analyze regulatory sequences from a large list of organisms. In these sequences, transcription factor binding sites can be detected and reported along with various statistic measurements and visualizations. Based on these binding sites and microarray expression data, ModuleMaster can detect cis-regulatory modules. The Program uses a multivariate evolutionary algorithm to detect not only significant combinations of binding sites, but also plausible expression correlation. As a result, you get a list of significant modules along with lots of information and opportunities to further evaluate and validate the module.

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