Related Experiment Videos
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee.
Fabrice Armougom1, Sébastien Moretti, Olivier Poirot
1Laboratoire Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR- 13288, Marseille cedex 09, France.
Nucleic Acids Research
|July 18, 2006
Summary
Expresso is a novel multiple sequence alignment server. It leverages structural information from protein databases to generate accurate alignments, enhancing biological sequence analysis.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Accurate multiple sequence alignment (MSA) is crucial for understanding protein function, evolution, and structure.
- Traditional sequence alignment methods can be limited when homology is low or structural information is not considered.
- Structure-based approaches offer improved accuracy for sequence alignment, especially for distantly related proteins.
Purpose of the Study:
- To introduce Expresso, a web server designed for automated, structure-guided multiple sequence alignment.
- To provide users with a tool that utilizes structural templates to improve alignment accuracy.
- To enable the alignment of user-provided sequences using homologous structures from the Protein Data Bank (PDB).
Main Methods:
- Expresso utilizes the Basic Local Alignment Search Tool (BLAST) to identify homologous sequences with known structures in the PDB.
- Identified PDB structures serve as templates to guide sequence alignment using methods such as SAP (Structure Alignment Program) or Fugue.
- An advanced mode allows for the use of private structures or user-specified PDB templates for enhanced control.
Main Results:
- Expresso generates multiple sequence alignments that incorporate structural information from identified templates.
- The server produces alignments with accuracy comparable to manual structure-based alignments when suitable structural information is available.
- The tool simplifies the process of obtaining structure-informed sequence alignments for researchers.
Conclusions:
- Expresso offers an effective and accessible method for performing accurate, structure-guided multiple sequence alignments.
- The server enhances the utility of sequence data by integrating structural context, aiding in biological interpretation.
- Expresso is a valuable resource for the bioinformatics community, available at http://www.tcoffee.org/.