A-040 On Computation of Minimum Free Energy and Partition Function of Multiple Nucleic Acid Sequences

概要

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Abstract. Given the base sequence of a DNA/RNA molecule, the folding problem is to predict the minimum free energy structure of the molecule. To capture the thermodynamic behavior of the molecule, its partition function is also required. These two functions, i.e., the fold function and the partition function, are implemented by dynamic programming in the Vienna RNA Package, which is widely used to analyze structures of DNA/RNA. However, the Vienna Package can only deal with a single sequence. In order to estimate interactions among multiple DNA/RNA molecules, we introduced virtual bases to concatenate multiple sequences into a single one, and extended the above two functions to cope with sequences containing virtual bases. The extensions have been successfully implemented as modifications to the Vienna RNA Package.
FIT(電子情報通信学会・情報処理学会)推進委員会の論文
2004-08-20