DIAL: A web server for the pairwise alignment of two RNA 3-dimensional structures using nucleotide, dihedral angle and base pairing similarities

Ferrè Fabrizzio 1 Yann Ponty 2, 3 William Lorenz 1 Peter Clote 1, *
* Corresponding author
2 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : 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 the Boltzmann pair probabilities for aligned positions within 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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https://hal.inria.fr/inria-00548870
Contributor : Yann Ponty <>
Submitted on : Monday, December 20, 2010 - 4:57:45 PM
Last modification on : Wednesday, March 27, 2019 - 4:41:29 PM

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Ferrè Fabrizzio, Yann Ponty, William Lorenz, Peter Clote. DIAL: A web server for the pairwise alignment of two RNA 3-dimensional structures using nucleotide, dihedral angle and base pairing similarities. Nucleic Acids Research, Oxford University Press, 2007, 35 (Web server issue), pp.W659--668. ⟨10.1093/nar/gkm334⟩. ⟨inria-00548870⟩

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