Our focus this summer is on RNA structure analysis methods. We are reading papers to understand analysis methods that quantify how similar two structures are to one another. Specifically, we are focusing on reading papers that describe methods that allow us to identify conserved or enrichment substructures across different RNAs, such as within precursor RNAs with alternatively spliced intron-exon junctions.
We are reading:
- How to benchmark RNA secondary structure prediction accuracy by Mathews DH. Methods. 2019 Jun 1;162-163:60-67. doi: 10.1016/j.ymeth.2019.04.003. Epub 2019 Apr 2. PMID: 30951834; PMCID: PMC7202366.
- RNAprofiling 2.0: Enhanced Cluster Analysis of Structural Ensembles by Hurley F, Heitsch C.J. Mol Biol. 2023 Mar 17:168047. doi: 10.1016/j.jmb.2023.168047. Epub ahead of print. PMID: 36933824.
- SHAPE-guided RNA structure homology search and motif discovery by Morandi E, van Hemert MJ, Incarnato D. Nat Commun. 2022 Mar 31;13(1):1722. doi: 10.1038/s41467-022-29398-y. PMID: 35361788; PMCID: PMC8971488.