FastMEDUSA: a parallelized tool to infer gene regulatory networks

Motivation: In order to construct gene regulatory networks of higher organisms from gene expression and promoter sequence data efficiently, we developed FastMEDUSA. In this parallelized version of the regulatory network-modeling tool MEDUSA, expression and sequence data are shared among a user-defined number of processors on a single multi-core machine or cluster. Our results show that FastMEDUSA allows a more efficient utilization of computational resources. While the determination of a regulatory network of brain tumor in Homo sapiens takes 12 days with MEDUSA, FastMEDUSA obtained the same results in 6 h by utilizing 100 processors. Availability: Source code and documentation of FastMEDUSA are available at https://wiki.nci.nih.gov/display/NOBbioinf/FastMEDUSA Contact: hfine@mail.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online.