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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:

PDF reprint of the paper:

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

 and "Supplementary Material".

Please send bug reports, questions, and comments to Barrett Foat (barrett AT and Gary Stormo (stormo AT

Source code for the latest version:    StructRED

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

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