Bi-alignments for incongruent RNA sequence and structure evolution
This paper introduces bi-alignments, a formal framework for cases where RNA sequence homology and RNA structural homology cannot be captured by the same alignment.
Showing only posts tagged RNA structure conservation. Show all posts.
Chikungunya virus phylogeny and lineage-specific RNA structures
An updated CHIKV phylogeny based on 598 genomes, linking lineage structure to conserved and lineage-specific 3' UTR RNA architectures.
Comparative genomics of flavivirus 3' UTR RNA structures
A comparative genomics analysis of flavivirus 3' UTRs that identifies conserved exoribonuclease-resistant RNAs and lineage-specific architectural variation across tick-borne, insect-specific, and no-known-vector flaviviruses.
How inverted SINEs repress gene expression
This paper shows that nearby inverted SINEs, especially Alu pairs in 3'UTRs, are associated with reduced gene expression and can repress transcripts by impairing RNA polymerase II elongation.
Predicting RNA structures from sequence and probing data
This review explains how classical thermodynamic RNA folding models can be improved with chemical probing data, and why that combination remains one of the most reliable routes to biologically useful structure prediction.
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