English
 
Help Privacy Policy Disclaimer
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences

Winkler, J., Urgese, G., Ficarra, E., & Reinert, K. (2022). LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences. BMC Bioinformatics, 23: 18. doi:10.1186/s12859-021-04532-7.

Item is

Basic

show hide
Genre: Journal Article

Files

show Files
hide Files
:
BMCBioinformatics_Winkler et al_2022.pdf (Publisher version), 3MB
Name:
BMCBioinformatics_Winkler et al_2022.pdf
Description:
-
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
© 2022, The Author(s)

Locators

show

Creators

show
hide
 Creators:
Winkler, Jörg, Author
Urgese, Gianvito , Author
Ficarra, Elisa , Author
Reinert, Knut1, Author              
Affiliations:
1Efficient Algorithms for Omics Data (Knut Reinert), Max Planck Fellow Group, Max Planck Institute for Molecular Genetics, Max Planck Society, ou_2385698              

Content

show
hide
Free keywords: -
 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 available software. Results We present the SeqAn-based software LaRA 2 that is significantly faster than comparable software for accurate pairwise and multiple alignments of structured RNA sequences. In contrast to other programs our approach can handle arbitrary pseudoknots. As an improved re-implementation of the LaRA tool for structural alignments, LaRA 2 uses multi-threading and vectorization for parallel execution and a new heuristic for computing a lower boundary of the solution. Our algorithmic improvements yield a program that is up to 130 times faster than the previous version. Conclusions With LaRA 2 we provide a tool to analyse large sets of RNA secondary structures in relatively short time, based on structural alignment. The produced alignments can be used to derive structural motifs for the search in genomic databases.

Details

show
hide
Language(s): eng - English
 Dates: 2021-12-132022-01-06
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1186/s12859-021-04532-7
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: BMC Bioinformatics
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: BioMed Central
Pages: - Volume / Issue: 23 Sequence Number: 18 Start / End Page: - Identifier: ISSN: 1471-2105
CoNE: https://pure.mpg.de/cone/journals/resource/111000136905000