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Related Concept Videos

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A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA
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Using ConSurf to Detect Functionally Important Regions in RNA.

Maya Rubin1, Nir Ben-Tal1

  • 1Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel.

Current Protocols
|October 7, 2021
PubMed
Summary
This summary is machine-generated.

ConSurf analysis of RNA functional regions is improved by constructing effective multiple sequence alignments (MSAs). New protocols enable successful evolutionary conservation analysis for diverse RNA molecules.

Keywords:
ConSurfRNA sequence analysisRate4Siteevolutionary analysisfunctional regions

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • The ConSurf web server uses evolutionary data to identify functional regions in proteins, assuming conserved regions evolve slowly.
  • While ConSurf is effective for protein analysis, its RNA analysis often fails due to insufficient homologous sequences and inadequate search tools.
  • Importing external multiple sequence alignments (MSAs) offers a workaround for ConSurf's limitations in RNA analysis.

Purpose of the Study:

  • To develop and validate protocols for constructing effective MSAs for RNA sequences.
  • To enable successful ConSurf evolutionary conservation analysis for RNA queries.

Main Methods:

  • Investigated various protocols for generating MSAs for RNA sequences.
  • Utilized ConSurf web server with both standard and external MSA approaches.
  • Tested protocols on a diverse set of RNA molecules.

Main Results:

  • The developed protocols significantly improve the ability to perform ConSurf analysis on RNA.
  • Successful evolutionary conservation analysis was achieved for various RNA molecules, overcoming previous data limitations.
  • Demonstrated the utility of external MSA construction for enhancing ConSurf's RNA analysis capabilities.

Conclusions:

  • Effective MSA construction is crucial for successful ConSurf evolutionary conservation analysis of RNA.
  • The presented protocols provide a viable solution for analyzing RNA functional regions using evolutionary data.
  • These methods enhance the application of ConSurf in RNA research.