Structural Alignment of RNA with Triple Helix Structure

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 ...

RNA structure and structural alignment

Structural Alignment of RNA with Complex Pseudoknot Structure

The secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature...

Multiple Structural RNA Alignment with Lagrangian Relaxation

In contrast to proteins, many classes of functionally related RNA molecules show a rather weak sequence conservation but instead a fairly well conserved secondary structure. Hence it is clear, that any method that relates RNA sequences in form of (multiple) alignments should take structural features into account. Since multiple alignments are of great importance for subsequent data analysis, re...

Structural Alignment of Pseudoknotted RNA

In this paper, we address the problem of discovering novel non-coding RNA (ncRNA) using primary sequence, and secondary structure conservation, focusing on ncRNA families with pseudoknotted structures. Our main technical result is an efficient algorithm for computing an optimum structural alignment of an RNA sequence against a genomic substring. This algorithm has two applications. First, by sc...