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Nucleic Acids Research 2005 33(Web Server Issue):W650-W653; doi:10.1093/nar/gki473
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© The Author 2005. Published by Oxford University Press. All rights reserved
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{at}oupjournals.org

Article

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

Jakob H. Havgaard, Rune B. Lyngsø1 and Jan Gorodkin*

Center for Bioinformatics and Division of Genetics, IBHV, The Royal Veterinary and Agricultural University Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark 1Department of Statistics, Oxford University 1 South Parks Road, Oxford OX1 3TG, UK

*To whom correspondence should be addressed: Tel: +45 3528 3578; Fax: +45 3528 3042; Email: gorodkin{at}bioinf.kvl.dk

Received February 14, 2005. Revised April 6, 2005. Accepted April 15, 2005.

FOLDALIGN is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of FOLDALIGN. The server can be used to scan two sequences for a common structural RNA motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. The web server can be accessed at http://foldalign.kvl.dk.


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