LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences.

ABSTRACT:

Background

The function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the molecule, formed by Watson-Crick interactions between nucleotides. Hence, modern RNA alignment algorithms routinely take structural information into account. In order to discover yet unknown RNA families and infer their possible functions, the structural alignment of RNAs is an essential task. This task demands a lot of computational resources, especially for aligning many long sequences, and it therefore requires efficient algorithms that utilize modern hardware when available. A subset of the secondary structures contains overlapping interactions (called pseudoknots), which add additional complexity to the problem and are often ignored in

SUBMITTER: Winkler J 

PROVIDER: S-EPMC8734264 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature