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

Area of Science:

• Bioinformatics
• Computational Biology
• Structural Biology

Background:

• Accurate RNA 3D structure alignment is crucial for understanding RNA function and evolution.
• Existing methods may not efficiently handle the complexities of RNA structural variations.

Purpose of the Study:

• To introduce DIAL (dihedral alignment), a novel web server for pairwise 3D RNA structural alignment.
• To provide efficient and comprehensive tools for RNA structural analysis and motif discovery.

Main Methods:

• Development of a dynamic programming algorithm considering dihedral angles, sequence, and base-pairing similarity.
• Implementation of global, local, and semiglobal (motif search) alignment algorithms.
• Inclusion of suboptimal alignment and Boltzmann pair probabilities calculation.

Main Results:

• DIAL achieves quadratic time complexity for RNA 3D structural alignment.
• The semiglobal alignment algorithm enables detection of contiguous or fragmented 3D RNA motifs.
• Graphical output allows interactive 3D superposition visualization of aligned structures.

Conclusions:

• DIAL offers a powerful and accessible platform for RNA 3D structure comparison and motif identification.
• The tool facilitates deeper insights into RNA structural relationships and functional elements.
• The web server is publicly available at http://bioinformatics.bc.edu/clotelab/DIAL.