Searching for alternate RNA structures in genomic sequences.
Proceedings of 1st workshop on Computational Methods for Structural RNAs (CMSR'14). isbn:978-2-9550187-0-5. pp. 13-24. doi:10.15455/CMSR.2014.0002
Abstract. We introduce the concept of RNA multi-structures, that is a formal grammar-based framework specifically designed to model a set of alternate RNA secondary structures. Such alternate structures can either be a set of suboptimal foldings, or distinct stable folding states, or variants within an RNA family. We provide several such examples and propose an efficient algorithm to search for RNA multi-structures within a genomic sequence.
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