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Related Experiment Videos

R-Coffee: a method for multiple alignment of non-coding RNA.

Andreas Wilm1, Desmond G Higgins, Cédric Notredame

  • 1The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland.

Nucleic Acids Research
|April 19, 2008
PubMed
Summary
This summary is machine-generated.

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R-Coffee enhances RNA sequence alignment accuracy by integrating secondary structure information. This tool improves existing methods and offers a robust protocol for aligning both short and long RNA sequences effectively.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Structural Bioinformatics

Background:

  • Accurate multiple RNA sequence alignment is crucial for understanding RNA function and evolution.
  • Existing methods often struggle to effectively incorporate RNA secondary structure information into alignments.
  • T-Coffee is a versatile alignment package, but a specialized version for RNA is needed.

Purpose of the Study:

  • To develop and evaluate R-Coffee, a multiple RNA sequence alignment package leveraging secondary structure.
  • To assess R-Coffee's performance as an alignment improver and its compatibility with other alignment methods.
  • To determine optimal protocols for aligning short and long RNA sequences using R-Coffee.

Main Methods:

  • R-Coffee was developed based on T-Coffee, incorporating a novel alignment-scoring scheme for secondary structure.

Related Experiment Videos

  • It was used to combine pairwise outputs from sequence and structural aligners.
  • Performance was evaluated on BRAliBase and Cmfinder datasets, comparing various R-Coffee combinations.

    • Main Results:

    • R-Coffee significantly improved the accuracy of all tested sequence aligners.
    • The consistency-based component of T-Coffee enhanced several structural aligners.
    • The optimal protocol for short sequences (<200 nt) was R-Coffee combined with the Consan structural aligner.
    • R-Coffee also demonstrated effectiveness for longer RNA sequences.

    Conclusions:

    • R-Coffee is a powerful tool for improving multiple RNA sequence alignment accuracy by utilizing secondary structure information.
    • The combination of R-Coffee with structural aligners like Consan provides highly accurate alignments for short RNAs.
    • R-Coffee offers a flexible and accurate solution for aligning diverse RNA datasets, including those typically challenging for structural aligners.