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R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

Jamie J Cannone1, Blake A Sweeney2, Anton I Petrov3

  • 1Institute for Cellular and Molecular Biology, and the Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA.

Nucleic Acids Research
|June 7, 2015
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Summary
This summary is machine-generated.

The R3D-2-MSA server links RNA 3D structures to multiple sequence alignments (MSAs). This tool provides access to curated ribosomal RNA alignments, aiding structural and evolutionary RNA research.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • RNA 3D structures and multiple sequence alignments (MSAs) are crucial for understanding RNA function and evolution.
  • Integrating structural and sequence data presents a significant challenge in bioinformatics.
  • Existing tools often lack seamless integration between 3D structural information and comprehensive MSAs.

Purpose of the Study:

  • To develop a novel web service, R3D-2-MSA, that bridges the gap between RNA 3D structures and high-quality MSAs.
  • To provide researchers with efficient access to curated ribosomal RNA (rRNA) sequence alignments linked to atomic-resolution 3D structures.
  • To offer both manual and programmatic access to facilitate diverse research applications.

Main Methods:

  • The R3D-2-MSA server utilizes curated, representative rRNA MSAs from bacterial, archaeal, eukaryal, and organellar sources.
  • It maps user-specified nucleotide ranges or positions from 3D structures to corresponding columns in the MSAs.
  • A web-based interface and an Application Program Interface (API) are provided for data access and retrieval.

Main Results:

  • The server successfully links RNA 3D structures to curated rRNA MSAs, enabling detailed sequence analysis.
  • Users can retrieve specific sequence segments based on structural coordinates, with options for browser display or JSON output.
  • The output includes interactive 3D visualizations, taxonomic information, and statistical summaries of sequence variants.

Conclusions:

  • R3D-2-MSA offers a valuable resource for researchers studying RNA structure-function relationships and evolution.
  • The seamless integration of 3D structural data with MSAs enhances the analysis of RNA sequence variations.
  • The freely accessible and user-friendly platform supports both manual exploration and automated data processing.