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RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure

Amir H Bayegan1, Peter Clote1

  • 1Biology Department, Boston College, Chestnut Hill, MA, United States of America.

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|January 25, 2020
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Summary
This summary is machine-generated.

RNAmountAlign is new C++ software for RNA sequence/structure alignment, offering accurate and fast homology identification. Its extension, RNAmountAlignScan, efficiently finds similar RNA sequences in genomes.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • RNA structural alignment is crucial for understanding molecular function and applications.
  • Existing RNA alignment tools often do not fully integrate sequence and structural information.
  • Accurate and efficient RNA alignment methods are needed for biological discovery.

Purpose of the Study:

  • To introduce RNAmountAlign, a novel C++ software for RNA sequence and structure alignment.
  • To develop an extension, RNAmountAlignScan, for efficient genome-wide scanning of structural RNA homologs.
  • To evaluate the performance of RNAmountAlign and RNAmountAlignScan against existing tools.

Main Methods:

  • RNAmountAlign utilizes incremental mountain height for structural information representation.
  • It implements a weighted combination of sequence and structural similarity for alignment.
  • The software supports pairwise local, global, semiglobal, and progressive multiple alignments.
  • RNAmountAlignScan performs genome scanning for sequence and structural similarity.

Main Results:

  • RNAmountAlign achieves O(n3) time and O(n2) space complexity for pairwise alignment.
  • Benchmarking shows RNAmountAlign offers competitive accuracy and faster runtimes than several established tools.
  • RNAmountAlignScan outperforms RSEARCH and sequence-only scans for genome-wide homology detection.

Conclusions:

  • RNAmountAlign provides an accurate and efficient solution for RNA sequence/structure alignment.
  • RNAmountAlignScan enhances the discovery of structurally similar RNAs within large genomic datasets.
  • These tools advance the field of RNA bioinformatics by integrating sequence and structural information effectively.