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

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 Boltzmann pair probabilities Pr(a(i),b(j)) for aligned positions a(i) , b(j) from the optimal alignment. If a non-zero suboptimal alignment score ratio is entered, then the semiglobal alignment algorithm may be used to detect str

SUBMITTER: Ferre F 

PROVIDER: S-EPMC1933154 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature