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The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment

Sebastien Moretti1, Fabrice Armougom, Iain M Wallace

  • 1Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL, CH-101 Lausanne.

Nucleic Acids Research
|May 29, 2007
PubMed
Summary
This summary is machine-generated.

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The M-Coffee server generates accurate multiple sequence alignments (MSAs) by integrating multiple MSA methods. This approach provides a consensus alignment with consistency scores, enhancing biological sequence analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Multiple sequence alignment (MSA) is crucial for understanding protein and DNA sequence relationships.
  • Existing MSA methods often require users to arbitrarily select a single tool, potentially missing optimal alignment strategies.

Purpose of the Study:

  • To develop a web server that combines multiple MSA methods for improved alignment accuracy.
  • To provide users with a consensus MSA and a measure of its reliability based on individual method contributions.

Main Methods:

  • The M-Coffee server utilizes a specialized mode of the T-Coffee package to compute consensus MSAs.
  • It accepts DNA or protein sequences in FASTA format as input.
  • The server integrates outputs from various chosen MSA methods.

Related Experiment Videos

Main Results:

  • M-Coffee generates a single, consensus multiple sequence alignment from multiple input methods.
  • The alignment is accompanied by a local estimation of its consistency relative to the individual MSAs.
  • The server supports common alignment output formats.

Conclusions:

  • M-Coffee offers a robust solution for generating reliable MSAs by leveraging the strengths of diverse alignment algorithms.
  • The tool enhances sequence analysis by providing a consensus alignment with confidence scores.
  • It is available as freeware, open-source, and accessible via a web service or standalone package.