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INTERALIGN: interactive alignment editor for distantly related protein sequences.

Olivier Pible1, Gilles Imbert, Jean-Luc Pellequer

  • 1Commissariat à I'Energie Atomique, CEA VALRTTO, DSV-DIEP-SBTN, Service de Biochimie post-génomique & Toxicologie Nucliaire Bagnols-sur-Cèze, France. olivier.pible@cea.fr

Bioinformatics (Oxford, England)
|May 5, 2005
PubMed
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Improving protein sequence alignment quality, especially in the twilight zone (<30% identity), is challenging. INTERALIGN software aids this by integrating structural views and profile alignment for better accuracy.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Multiple sequence alignment (MSA) quality assessment is crucial for protein sequence analysis.
  • Aligning protein sequences with low identity (<30%, the 'twilight zone') presents significant challenges.

Purpose of the Study:

  • To introduce INTERALIGN, a user-friendly alignment editor designed to improve MSA quality.
  • To facilitate the alignment of protein sequences, particularly those with low homology, by incorporating structural information.

Main Methods:

  • Developed INTERALIGN, featuring secondary structure visualization and synchronized C-alpha trace display of protein structures.
  • Implemented profile alignment using CLUSTALW to enhance alignment accuracy.
  • Utilized tree-based ordering to aid in identifying structurally similar sequences.

Related Experiment Videos

Main Results:

  • INTERALIGN provides a synchronized view of structural and sequence alignments.
  • Profile alignment within INTERALIGN improves alignment quality compared to standard MSAs, especially for low-identity sequences.
  • Tree-based ordering assists in finding the closest structural matches.

Conclusions:

  • INTERALIGN offers a practical solution for improving and assessing MSA quality, particularly for challenging twilight zone sequences.
  • The integration of structural data and profile alignment significantly enhances the reliability of protein sequence analysis.