ECSFinder: optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences.

ABSTRACT: Accurate prediction of RNA secondary structures is essential for understanding the evolutionary conservation and functional roles of long noncoding RNAs (lncRNAs) across diverse species. In this study, we benchmarked two leading tools for predicting evolutionarily conserved RNA secondary structures (ECSs), SISSIz and R-scape, using two distinct experimental frameworks: one focusing on well-characterized mitochondrial RNA structures and the other on experimentally validated Rfam structures embedded within simulated genome alignments. While both tools performed similarly overall, each displayed subtle preferences in detecting ECSs. To overcome their individual limitations, we evaluated two interpretable machine learning approaches that integrate the strengths of both methods. By balancing th

SUBMITTER: Gaonac'h-Lovejoy V 

PROVIDER: S-EPMC12370627 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature