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Bioinformatics Advance Access originally published online on May 3, 2005
Bioinformatics 2005 21(14):3166-3167; doi:10.1093/bioinformatics/bti474
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

INTERALIGN: interactive alignment editor for distantly related protein sequences

Olivier Pible *, Gilles Imbert and Jean-Luc Pellequer

Commissariat à I'Energie Atomique, CEA VALRTTO, DSV-DIEP-SBTN, Service de Biochimie post-génomique & Toxicologie Nucliaire Bagnols-sur-Cèze, France

*To whom correspondence should be addressed.

Summary: Improving and ascertaining the quality of a multiple sequence alignment is a very challenging step in protein sequence analysis. This is particularly the case when dealing with sequences in the ‘twilight zone’, i.e. sharing <30% identity. Here we describe INTERALIGN, a dedicated user-friendly alignment editor including a view of secondary structures and a synchronized display of carbon alpha traces of corresponding protein structures. Profile alignment, using CLUSTALW, is implemented to improve the alignment of a sequence of unknown structure with the visually optimized structural alignment as compared with a standard multiple sequence alignment. Tree-based ordering further helps in identifying the structure closest to a given sequence.

Availability: Windows and Linux packages, as well as source files, are available under the CeCILL free software licensing agreement at the following address: http://www-dsv.cea.fr/content/cea/d_dep/d_diep/d_sbtn/download.htm

Contact: olivier.pible{at}cea.fr

Received on January 14, 2005; revised on April 11, 2005; accepted on April 25, 2005

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