2 research outputs found
Structural alignment of RNA with triple helix structure
Structural alignment is useful in identifying members of ncRNAs. Existing tools are all based on the secondary structures of the molecules. There is evidence showing that tertiary interactions (the interaction between a single-stranded nucleotide and a base-pair) in triple helix structures are critical in some functions of ncRNAs. In this article, we address the problem of structural alignment of RNAs with the triple helix. We provide a formal definition to capture a simplified model of a triple helix structure, then develop an algorithm of O(mn(3)) time to align a query sequence (of length m) with known triple helix structure with a target sequence (of length n) with an unknown structure. The resulting algorithm is shown to be useful in identifying ncRNA members in a simulated genome. © Copyright 2012, Mary Ann Liebert, Inc. 2012.published_or_final_versio
Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots
We present a general setting for structure-sequence comparison in a large
class of RNA structures that unifies and generalizes a number of recent works
on specific families on structures. Our approach is based on tree decomposition
of structures and gives rises to a general parameterized algorithm, where the
exponential part of the complexity depends on the family of structures. For
each of the previously studied families, our algorithm has the same complexity
as the specific algorithm that had been given before.Comment: (2012