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R-Coffee: a web server for accurately aligning noncoding RNA sequences.

Sébastien Moretti1, Andreas Wilm, Desmond G Higgins

  • 1Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland.

Nucleic Acids Research
|May 17, 2008
PubMed
Summary
This summary is machine-generated.

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The R-Coffee web server accurately aligns noncoding RNA (ncRNA) sequences using predicted secondary structures. It offers accurate and fast modes for various dataset sizes, improving ncRNA analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Accurate multiple sequence alignment (MSA) is crucial for understanding noncoding RNA (ncRNA) function.
  • Existing methods often struggle to incorporate ncRNA secondary structure information effectively.
  • The T-Coffee package provides a framework for integrating diverse alignment strategies.

Purpose of the Study:

  • To develop and present the R-Coffee web server for highly accurate ncRNA multiple sequence alignment.
  • To incorporate predicted secondary structures into the alignment process.
  • To offer distinct modes for optimizing alignment accuracy and speed based on dataset characteristics.

Main Methods:

  • R-Coffee utilizes a novel algorithm within the T-Coffee package, combining pairwise and multiple sequence alignment (MSA) methods.

Related Experiment Videos

  • It computes an MSA consistent with an input alignment library and predicted secondary structures, using RNAplfold for prediction.
  • Two modes are offered: a slow/accurate mode (R-Coffee/Consan) for small datasets and a fast mode (RM-Coffee) for larger datasets, integrating top-performing RNA aligners (MUSCLE, MAFFT, ProbConsRNA).

    • Main Results:

    • The R-Coffee/Consan combination demonstrates high accuracy for short ncRNA sequences, benchmarking as one of the best available methods.
    • The RM-Coffee mode provides comparable alignment results for longer sequences, offering a faster alternative.
    • BRAliBase benchmarks validate the performance of both R-Coffee modes.

    Conclusions:

    • The R-Coffee web server provides a significant advancement in accurate ncRNA sequence alignment by integrating secondary structure information.
    • It offers flexible and validated solutions for both small and large-scale ncRNA alignment challenges.
    • The server is accessible at http://www.tcoffee.org, facilitating broader research in ncRNA analysis.