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Nucleic Acids Research Advance Access published online on May 30, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn321
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MAGNOLIA: multiple alignment of protein–coding and structural RNA sequences

Arnaud Fontaine, Antoine de Monte and Hélène Touzet*

LIFL (UMR CNRS 8022 Université Lille 1) – INRIA Lille-Nord Europe

*To whom correspondence should be addressed. Tel: (33) 3 59 57 79 16; Fax: (33) 3 59 57 78 50; Email: Helene.Touzet{at}lifl.fr

Received January 31, 2008. Revised April 26, 2008. Accepted May 7, 2008.

MAGNOLIA is a new software for multiple alignment of nucleic acid sequences, which are recognized to be hard to align. The idea is that the multiple alignment process should be improved by taking into account the putative function of the sequences. In this perspective, MAGNOLIA is especially designed for sequences that are intended to be either protein-coding or structural RNAs. It extracts information from the similarities and differences in the data, and searches for a specific evolutionary pattern between sequences before aligning them. The alignment step then incorporates this information to achieve higher accuracy. The website is available at http://bioinfo.lifl.fr/magnolia.


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