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Nucleic Acids Research Advance Access originally published online on June 13, 2007
Nucleic Acids Research 2007 35(Web Server issue):W659-W668; doi:10.1093/nar/gkm334
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W659-W668
© 2007 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.

Articles

DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities

F. Ferrè1, Y. Ponty2, W. A. Lorenz2 and Peter Clote2,*

1Harvard Medical School, Children's Hospital, Hematology/Oncology Department, Boston, MA 02115 and 2Department of Biology, Boston College, Chestnut Hill, MA 02467, USA

*To whom correspondence should be addressed. Tel: +1 617 552 1332; Fax: +1 617 552 2011; Email: clote{at}bc.edu

Received January 31, 2007. Revised April 15, 2007. Accepted April 18, 2007.

DIAL (dihedral alignment) is a web server that provides public access to a new dynamic programming algorithm for pairwise 3D structural alignment of RNA. DIAL achieves quadratic time by performing an alignment that accounts for (i) pseudo-dihedral and/or dihedral angle similarity, (ii) nucleotide sequence similarity and (iii) nucleotide base-pairing similarity.

DIAL provides access to three alignment algorithms: global (Needleman–Wunsch), local (Smith–Waterman) and semiglobal (modified to yield motif search). Suboptimal alignments are optionally returned, and also Boltzmann pair probabilities Pr(ai,bj) for aligned positions ai , bj from the optimal alignment. If a non-zero suboptimal alignment score ratio is entered, then the semiglobal alignment algorithm may be used to detect structurally similar occurrences of a user-specified 3D motif. The query motif may be contiguous in the linear chain or fragmented in a number of noncontiguous regions.

The DIAL web server provides graphical output which allows the user to view, rotate and enlarge the 3D superposition for the optimal (and suboptimal) alignment of query to target. Although graphical output is available for all three algorithms, the semiglobal motif search may be of most interest in attempts to identify RNA motifs. DIAL is available at http://bioinformatics.bc.edu/clotelab/DIAL.


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