Journal
GENOME BIOLOGY
Volume 22, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-021-02379-y
Keywords
Hidden Markov model; High-throughput RNA structure probing; RNA structural changes
Funding
- Medical Research Council [MR/R008205/1]
- MRC [MR/R008205/1] Funding Source: UKRI
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The diffBUM-HMM model accurately detects RNA flexibility and conformational changes from high-throughput RNA structure-probing data, accounting for noise and variability. It demonstrates higher sensitivity than existing methods and is robust against false positives, showing its value in quantitatively detecting RNA structural changes and RNA-binding protein binding sites.
Advancing RNA structural probing techniques with next-generation sequencing has generated demands for complementary computational tools to robustly extract RNA structural information amidst sampling noise and variability. We present diffBUM-HMM, a noise-aware model that enables accurate detection of RNA flexibility and conformational changes from high-throughput RNA structure-probing data. diffBUM-HMM is widely compatible, accounting for sampling variation and sequence coverage biases, and displays higher sensitivity than existing methods while robust against false positives. Our analyses of datasets generated with a variety of RNA probing chemistries demonstrate the value of diffBUM-HMM for quantitatively detecting RNA structural changes and RNA-binding protein binding sites.
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