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3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment.

Olivier Poirot1, Karsten Suhre, Chantal Abergel

  • 1Information Génomique et Structurale UPR2589-CNRS, CNRS, 31, Chemin Joseph Aiguier, 13 402 Marseille Cedex 20, France.

Nucleic Acids Research
|June 25, 2004
PubMed
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This study introduces 3D-Coffee@igs, a web tool for high-quality multiple sequence alignments (MSAs). It enhances alignment accuracy by integrating protein sequences and structures using advanced algorithms.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Bioinformatics

Background:

  • Multiple Sequence Alignments (MSAs) are crucial for understanding protein function and evolution.
  • Integrating structural information can improve the accuracy of MSAs, especially for distantly related proteins.
  • Existing MSA tools often do not effectively leverage available protein structure data.

Purpose of the Study:

  • To present 3D-Coffee@igs, a novel web-based tool for computing high-quality MSAs.
  • To enable the integration of both protein sequences and 3D structures for enhanced alignment accuracy.
  • To provide a user-friendly platform for researchers to generate accurate MSAs.

Main Methods:

  • 3D-Coffee@igs combines protein sequences with 3D structural information.

Related Experiment Videos

  • Protein structures can be input as PDB identifiers or uploaded directly.
  • Pairwise structure alignment is performed using SAP, and sequence-structure alignment uses Fugue.
  • The T-Coffee algorithm integrates these pairwise alignments into a final MSA.

    • Main Results:

    • 3D-Coffee@igs successfully computes high-quality multiple sequence alignments.
    • The integration of structural data demonstrably increases alignment accuracy.
    • The web server provides a practical and accessible solution for MSA generation.

    Conclusions:

    • 3D-Coffee@igs represents a significant advancement in MSA computation by incorporating structural data.
    • The tool enhances the reliability of evolutionary and functional inferences derived from MSAs.
    • Researchers can utilize 3D-Coffee@igs to improve the accuracy of their sequence and structure-based analyses.