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2006
IEEE

Simplicity in RNA Secondary Structure Alignment: Towards biologically plausible alignments

9 years 7 months ago
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...
Rimon Mikhaiel, Guohui Lin, Eleni Stroulia
Added 10 Jun 2010
Updated 10 Jun 2010
Type Conference
Year 2006
Where BIBE
Authors Rimon Mikhaiel, Guohui Lin, Eleni Stroulia
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