SCOPE (Suite for Computational identification Of Promoter Elements) is an ensemble of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences.The SCOPE motif finder is designed to identify candidate regulatory DNA motifs from sets of genes that are coordinately regulated. SCOPE motif finder uses an ensemble of three programs behind the scenes to identify different kinds of motifs – BEAM identifies nondegenerate motifs (e.g. ACGTGC), PRISM identifies degenerate motifs (e.g. AWCGRYH), and SPACER identifies bipartite motifs (e.g. ACCNNNNNNNNNGTT). All parameters are automatically set to find the optimal length motif and degree of degeneracy in the reported motifs.
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Chakravarty, A, Carlson, JM, Khetani, RS, and Gross, RH,
“A novel ensemble learning method for de novo computational identification of DNA binding sites.”
BMC Bioinformatics 8: 249 (2007)