IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling

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Hardouin, Pierre | Pan, Nan | Du Moutier, Francois-Xavier Lyonnet | Chamond, Nathalie | Ponty, Yann | Will, Sebastian | Sargueil, Bruno

Edité par CCSD ; Oxford University Press -

International audience. In addition to their sequence, multiple functions of RNAs are encoded within their structure, which is often difficult to solve using physico-chemical methods. Incorporating low resolution experimental data such as chemical probing into computational prediction significantly enhances RNA structure modeling accuracy. While medium and high-throughput RNA structure probing techniques are widely accessible, the subsequent analysis process can be cumbersome, involving multiple software and manual data manipulation. In addition, the relevant interpretation of the data requires proper parametrization of the software and a strict consistency in the analysis pipeline. To streamline such workflows, we introduce IPANEMAP Suite, a comprehensive platform that guides users from chemical probing raw data to visually informative secondary structure models. IPANEMAP Suite seamlessly integrates various experimental data sets and facilitates comparative analysis of RNA structures under different conditions (footprinting), aiding in the study of protein or small molecule interactions with RNA. Here we show that the unique ability of IPANEMAP suite to perform integrative modeling using several chemical probing datasets with phylogenetic data can be instrumental to obtain accurate secondary structure models. The platform's project-based approach ensures full-traceability and generates publication-quality outputs, simplifying the entire RNA structure analysis process. IPANEMAP Suite is freely available at https://github.com/Sargueil-CiTCoM/ipasuite under an GPL-3.0 licence.

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