Cistematic is a Python package with a rich set of API’s that simplify the collection and analysis of candidate cis-regulatory elements from a number of different motif-finding programs such as Meme, and cisGreedy (built-in). Cistematic assesses the significance of each motif by comparing it to its prevalence genome-wide.
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Genome Res. 2006 Oct;16(10):1208-21. Epub 2006 Sep 8.
Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.
Mortazavi A, Leeper Thompson EC, Garcia ST, Myers RM, Wold B.