Here, we provide a new software tool, called FastBill, for prediction of evolutionarily conserved cis-regulatory modules. It improves on the previous version of our program, called Billboard, by improving the statistical significance calculation. It is also faster than the original Billboard, allowing for large-scale analyses, including multiple informant species. We illustrate the utility of FastBill by performing a large-scale computational experiment of enhancer prediction in the promoter area of more than 150 Drosophila melanogaster genes that possess annotated experimentally verified enhancers. FastBill is written in Python and is freely available for download as a standalone tool.
Keywords: CRM; arrangement of transcription factor binding sites; computational prediction of enhancers; evolutionary conservation.