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Bioinformatics 2006 22(14):e35-e39; doi:10.1093/bioinformatics/btl218
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

The iRMSD: a local measure of sequence alignment accuracy using structural information

Fabrice Armougom 1, Sébastien Moretti 1, Vladimir Keduas 1 and Cedric Notredame 1,*

1 Laboratoire Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM) Parc Scientifique de Luminy, case 934, 163 Avenue de Luminy, FR-13288, Marseille cedex 09

*To whom correspondence should be addressed.

Motivation: We introduce the iRMSD, a new type of RMSD, independent from any structure superposition and suitable for evaluating sequence alignments of proteins with known structures.

Results: We demonstrate that the iRMSD is equivalent to the standard RMSD although much simpler to compute and we also show that it is suitable for comparing sequence alignments and benchmarking multiple sequence alignment methods. We tested the iRMSD score on 6 established multiple sequence alignment packages and found the results to be consistent with those obtained using an established reference alignment collection like Prefab.

Availability: The iRMSD is part of the T-Coffee package and is distributed as an open source freeware (http://www.tcoffee.org/).

Contact: cedric.notredame{at}europe.com; cedric.notredame{at}igs.cnrs-mrs.fr


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