June 15, 2016 (Vol. 36, No. 12)
Strong Points: Free to download, nice tool introductions on the website
Weak Points: Requires some familiarity with Python
The Computational Biology and Bioinformatics Research group at RWTH University in Germany has provided a number of useful tools for scientists studying gene regulatory networks (that is, researchers in the field of “regulatory genomics”). The tools—all written in Python—collectively constitute the Regulatory Genomics Toolbox and can be found on the website of the same name. There are six resources in all. These include HINT—a tool to detect transcription factor binding in open chromatin regions through the identification and integration of DNA footprints from DNAse-Seq data and histone modifications from ChIP-Seq data—as well as a motif analysis tool to identify binding sites. Other tools facilitate visualization of genomic data, assess the triple helix potential of DNA and RNA regions, and analyze peaks in ChIP-Seq data. The source code for each of the tools is free to download, and the website provides a brief introduction to each tool included in this virtual toolbox.