Introduction

RNA Structurome Quantification (RSQ) (This wiki is under construction)

RSQ is a Python based package for RNA structure profiling data analysis.

• It accepts RNA structure profiling data generated from SHAPE-Seq, PARS and DMS-Seq technologies.
• It can fold multiple secondary structures for each transcript based on user defined constraints.
• It could quantify the abundance of each structure centroid using the RNA structure profiling data.
• It provides a series of commands for users to customize every procedure.
• It could handle RNA structure profiling data generated from gene isoforms or overlapped transcripts.

RNA Structure Profiling Technologies

Current well-known RNA structure profiling technologies include:

• PARS
• DMS-Seq
• SHAPE-Seq
• Frag-Seq
• et. al.

A demo figure for PARS technology

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RSQ Analysis Logic

Two dynamics of RNA structurome

• Gene transcription dynamics: Alternative splicing, Dynamic usage of promoters
• RNA conformation dynamics: RNA form multiple conformations in cell

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© 2013, Yunfei Wang (yfwang0405ATgmail.com), The University of Texas at Dallas