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• What is StructRED? 

  
  

  Structural Cis-Regulatory Element Detector (StructRED) 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. It was developed by Barrett Foat and Gary Stormo at Washington University in Saint Louis.

The algorithm interrogates a motif search space (composed of combinations of small stem-loop structures and specific sequence information) for how well their occurrences in mRNA sequences predict corresponding measurements of mRNA levels from functional genomics experiments. StructRED then builds a linear model of several stem-loop motifs that significantly explain mRNA levels in the input data set. Inputs to StructRED are a fasta sequence file and one or more columns of numerical mRNA level data in tab-delimited text files.

Some advantages of this method are that it:

• Detects cis-regulatory elements that are defined by both nucleotide sequence and RNA secondary structure

• Requires no thresholding of microarray data

• Does not require a "positive" or "negative" sequence set
  

PDF reprint of the paper:

"Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs"

 and "Supplementary Material".

• Questions and Comments?

Please send bug reports, questions, and comments to Barrett Foat (barrett AT wustl.edu) and Gary Stormo (stormo AT genetics.wustl.edu).

• Download StructRED 

Source code for the latest version:    StructRED

Last updated June 2, 2009. Thanks to Xing Xu for the website template.