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Related Experiment Videos

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

Jörg Winkler1,2, Gianvito Urgese3, Elisa Ficarra4

  • 1Department of Mathematics and Computer Science, Free University Berlin, Takustraße 9, 14195, Berlin, Germany. j.winkler@fu-berlin.de.

BMC Bioinformatics
|January 7, 2022
PubMed
Summary

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This summary is machine-generated.

LaRA 2 is a new RNA structural alignment tool that is up to 130 times faster than previous versions. It accurately aligns structured RNA sequences, including those with complex pseudoknots, enabling faster discovery of RNA families and functions.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Non-coding RNA function is dictated by spatial conformation (secondary structure) via Watson-Crick interactions.
  • Accurate RNA structural alignment is crucial for discovering novel RNA families and their functions.
  • Existing algorithms are computationally intensive, especially for long sequences, and often ignore pseudoknots.

Purpose of the Study:

  • To develop a significantly faster and more accurate software for pairwise and multiple structural alignments of RNA sequences.
  • To incorporate the handling of arbitrary pseudoknots, which are often omitted in current software.
  • To leverage modern hardware through parallel execution techniques.

Main Methods:

  • Development of LaRA 2, a SeqAn-based software, as an improved re-implementation of the LaRA tool.
Keywords:
AlgorithmsBioinformaticsInteger linear programParallel computingRNARNA secondary structureStructural alignment

Related Experiment Videos

  • Implementation of multi-threading and vectorization for parallel processing.
  • Introduction of a novel heuristic for calculating a lower bound of the solution.

    • Main Results:

    • LaRA 2 demonstrates significantly improved speed compared to comparable software for RNA structural alignment.
    • The software achieves up to a 130-fold increase in speed over its predecessor.
    • LaRA 2 accurately aligns structured RNA sequences and handles arbitrary pseudoknots.

    Conclusions:

    • LaRA 2 provides an efficient tool for analyzing large sets of RNA secondary structures rapidly.
    • The structural alignments generated by LaRA 2 can be used to derive structural motifs for genomic database searches.
    • This advancement facilitates quicker identification and functional annotation of RNA molecules.