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Related Experiment Videos

APDB: a web server to evaluate the accuracy of sequence alignments using structural information.

Fabrice Armougom1, Olivier Poirot, Sébastien Moretti

  • 1CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR-13288, Marseille cedex 09, France.

Bioinformatics (Oxford, England)
|October 13, 2006
PubMed
Summary
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The APDB webserver evaluates sequence alignments using known protein structures, providing scores for overall and local accuracy. It is a valuable tool for bioinformatics sequence analysis.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • APDB is part of the T-Coffee suite of tools.
  • It is available on www.tcoffee.org.
  • A freeware open-source stand-alone version is also available.

Purpose of the Study:

  • To evaluate sequence alignment accuracy using structural information.
  • To provide both overall and local evaluation scores for alignments.

Main Methods:

  • Utilizes structural information of proteins.
  • Analyzes sequence alignments containing at least two proteins with known structures.
  • Ignores sequences without known structures in the scoring procedure.

Main Results:

Related Experiment Videos

  • Returns a score correlated to overall alignment accuracy.
  • Provides a local evaluation of alignment quality.

Conclusions:

  • APDB is a webserver for assessing sequence alignment quality based on protein structures.
  • It offers a method for evaluating alignments when structural data is available.