DIAL (dihedral alignment) is a web server that provides public access to a new dynamic programming algorithm for structural alignment of RNA. DIAL achieves quadratic time by performing an alignment which accounts for (i) nucleotide sequence similarity (ii) dihedral angle similarity, (iii) nucleotide base-pairing similarity. Nucleotide sequences are extracted from user-uploaded PDB files, while DIAL computes the relevant dihedral angles. Instead of uploading a PDB file, instead the user can give the 4 character alphanumeric PDB code, and DIAL retrieves the PDB file from a local copy of the PDB.

DIAL provides access to three alignment algorithms: global (Needleman-Wunsch), local (Smith-Waterman) and global-semiglobal (motif search). Given a query structural motif, the latter algorithm may be used to detect structurally similar regions in the target structure. The DIAL web server provides graphical output which allows the user to view and rotate the 3-dimensional superposition for the optimal alignment of query to target. Although graphical output is available for all three algorithms, the global-semiglobal motif search may be of most interest in attempts to identify RNA motifs.

If you use the DIAL web server for your work, please cite the following reference.

DIAL: A web server for RNA structural alignment using dihedral angles
F. Ferre, W.A. Lorenz, Y. Ponty, P. Clote
submitted (2007)
Python programs designed by P. Clote and F. Ferre, implemented by F. Ferre, W.A. Lorenz and Y. Ponty. Web server developed by V. Chistyakov, F. Ferre, Y. Ponty, J. Persampieri.

This material is based upon work supported by the National Science Foundation under Grant No. 0543506. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.