StructRED (Structural Cis-Regulatory Element Detector) is an alignment-free algorithm that discovers secondary structure-defined cis-regulatory elements in mRNAs by modeling the effects that their occurrences exert on quantitative measurements of mRNA behavior in the form of microarray data.
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Barrett Foat and Gary D. Stormo
Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs
Mol. Syst. Biol. 2009. 5:268.