Simplicity in RNA Secondary Structure Alignment: Towards biologically plausible alignments

Ribonucleic acid (RNA) molecules contain the genetic information that regulates the functions of organisms. Given two different molecules, a preserved function corresponds to a preserved secondary RNA structure. Hence, RNA secondary-structure comparison is essential in predicting the functions of a newly discovered molecule. In this paper, we discuss our SPRC method for RNA structure comparison. In this work, we developed, a novel tree representation of RNA that reflects both its primary and secondary structure and a tree-alignment algorithm, which, given the tree representations of two RNA molecules, produces a sequence of mutations that could transform one RNA molecule to the other. Our SPRC algorithm extends the Zhang-Shasha tree-edit distance calculation algorithm in two ways: first, in addition to the distance, it reports all editing sequences with the same minimum edit cost, and second, it uses a biologically-inspired affine cost function. Furthermore, the SPRC method proposes s...

• Type: Conference
• Year: 2006
• Where: BIBE
• Authors: Rimon Mikhaiel, Guohui Lin, Eleni Stroulia
• Keywords: BIBE 2006, Bioinformatics, RNA Molecule, Rna Structure, SPRC Method