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Biochemistry, Biophysics, and Structural Biology Commons

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Retrospective Theses and Dissertations

2006

Computer Sciences

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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

A Modular Data Analysis Pipeline For The Discovery Of Novel Rna Motifs , Justin Schonfeld Jan 2006

A Modular Data Analysis Pipeline For The Discovery Of Novel Rna Motifs , Justin Schonfeld

Retrospective Theses and Dissertations

This dissertation presents a modular software pipeline that searches collections of RNA sequences for novel RNA motifs. In this case the motifs incorporate elements of primary and secondary structure. The motif search pipeline breaks up sets of RNA sequences into shortened segments of RNA primary sequence. The shortened segments are then folded to obtain low energy secondary structures. The distance estimation module of the pipeline then calculates distances between the folded bricks, and then analyzes the resulting distance matrices for patterns;An initial implementation of the pipeline is applied to synthetic and biological data sets. This implementation introduces a new ...