CrmMiner is designed to mine for cis-regulatory modules (CRMs) in a large number of sequences. Hence, it has the potential to find CRMs thousands of nucleotides away from their target TSSs.
Hani Zakaria Girgis, PhD
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BMC Bioinformatics. 2012 Feb 7;13:25. doi: 10.1186/1471-2105-13-25.
Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs.
Girgis HZ, Ovcharenko I.