Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.

ABSTRACT: RNAs perform their function by forming specific structures, which can change across cellular conditions. Structure probing experiments combined with next generation sequencing technology have enabled transcriptome-wide analysis of RNA secondary structure in various cellular conditions. Differential analysis of structure probing data in different conditions can reveal the RNA structurally variable regions (SVRs), which is important for understanding RNA functions. Here, we propose DiffScan, a computational framework for normalization and differential analysis of structure probing data in high resolution. DiffScan preprocesses structure probing datasets to remove systematic bias, and then scans the transcripts to identify SVRs and adaptively determines their lengths and locations. The propos

SUBMITTER: Yu B 

PROVIDER: S-EPMC9307511 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature