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Bioinformatics Advance Access published online on May 3, 2005
Bioinformatics, 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@oupjournals.org
Received January 14, 2005
Revised April 11, 2005
Accepted April 25, 2005

Applications note

INTERALIGN: interactive alignment editor for distantly related protein sequences

Olivier Pible 1*, Gilles Imbert 1, and Jean-Luc Pellequer 1

1 CEA, DIEP/SBTN, Bagnols sur Ceze, France

* To whom correspondence should be addressed.
Olivier Pible, E-mail: olivier.pible{at}cea.fr


  Abstract

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 "twighlight zone" i.e. sharing less than 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-optimised structural alignment as compared to a standard multiple sequence alignment. A tree-based ordering 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.


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