IPANEMAP: integrative probing analysis of nucleic acids empowered by multiple accessibility profiles.

ABSTRACT: The manual production of reliable RNA structure models from chemical probing experiments benefits from the integration of information derived from multiple protocols and reagents. However, the interpretation of multiple probing profiles remains a complex task, hindering the quality and reproducibility of modeling efforts. We introduce IPANEMAP, the first automated method for the modeling of RNA structure from multiple probing reactivity profiles. Input profiles can result from experiments based on diverse protocols, reagents, or collection of variants, and are jointly analyzed to predict the dominant conformations of an RNA. IPANEMAP combines sampling, clustering and multi-optimization, to produce secondary structure models that are both stable and well-supported by experimental evidences.

SUBMITTER: Saaidi A 

PROVIDER: S-EPMC7470984 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature