DIAL is a web server for 3-dimensional RNA structural alignment (global and local) and for motif detection. DIAL (DIhedral ALignment) runs in time that is quadratic in input length by performing an alignment which accounts for (i) pseudo-dihedral and/or dihedral angle similarity, (ii) nucleotide sequence similarity, (iii) nucleotide base-pairing similarity.
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F. Ferre; Y. Ponty; W. A. Lorenz; Peter Clote
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities ,
Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W659-68. Epub 2007 Jun 13.