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Identifying RNA contacts from SHAPE-MaP by partial correlation analysis

Tambe, Akshay and Doudna, Jennifer and Pachter, Lior (2014) Identifying RNA contacts from SHAPE-MaP by partial correlation analysis. . (Submitted)

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In a recent paper Siegfried et al. published a new sequence-based structural RNA assay that utilizes mutational profiling to detect base pairing (MaP). Output from MaP provides information about both pairing (via reactivities) and contact (via correlations). Reactivities can be coupled to partition function folding models for structural inference, while correlations can reveal pairs of sites that may be in structural proximity. The possibility for inference of 3D contacts via MaP suggests a novel approach to structural prediction for RNA analogous to covariance structural prediction for proteins. We explore this approach and show that partial correlation analysis outperforms na\"ive correlation analysis. Our results should be applicable to a wide range of high-throughput sequencing based RNA structural assays that are under development.

Item Type:Report or Paper (Discussion Paper)
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URLURL TypeDescription Paper
Pachter, Lior0000-0002-9164-6231
Record Number:CaltechAUTHORS:20170307-101642083
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74841
Deposited By: Tony Diaz
Deposited On:07 Mar 2017 18:33
Last Modified:24 Feb 2020 10:30

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