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.
Stormo Lab in Department of Genetics, Washington University
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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.