PhyloRNA: a database of RNA secondary structures with associated phylogenies

Abstract

The ability to access, search, and analyse large collections of RNA molecules together with their secondary structure and evolutionary context is essential for comparative and phylogeny-driven studies. Although RNA secondary structure is known to be more conserved than primary sequence, no existing resource systematically associates individual RNA molecules with curated phylogenetic classifications. Here, we introduce PhyloRNA, a curated meta-database that provides large-scale access to RNA secondary structures collected from public resources or derived from experimentally resolved 3D structures. PhyloRNA allows users to search, select, and download extensive sets of RNA molecules in multiple textual formats, each entry being explicitly linked to phylogenetic annotations derived from five curated taxonomy systems. In addition to taxonomic information, each RNA molecule is accompanied by a rich set of descriptors, including pseudoknot order, genus, and three levels of structural abstraction--Core, Core Plus, and Shape--which facilitate comparative analyses across sets of molecules. PhyloRNA is publicly available at https://bdslab.unicam.it/phylorna/ and is regularly updated to incorporate newly available data and revised taxonomic annotations.