Similar experience in DNA/genome analysis. A large part of DNA analysis was based on parser theory.
This paper was my introduction to DNA analysis as well as Chomsky hierarchy: https://www.jstor.org/stable/29774782 (I wasn't able to find a free copy).
IIRC, pseudoknots in RNA require context-free grammars to parse.
This paper was my introduction to DNA analysis as well as Chomsky hierarchy: https://www.jstor.org/stable/29774782 (I wasn't able to find a free copy).
IIRC, pseudoknots in RNA require context-free grammars to parse.