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JCB
2007

A Dynamic Programming Approach for Finding Common Patterns in RNAs

9 years 6 months ago
A Dynamic Programming Approach for Finding Common Patterns in RNAs
We developed a dynamic programming approach of computing common sequence structure patterns among two RNAs given their primary sequences and their secondary structures. Common patterns between two RNAs are defined to share the same local sequential and structural properties. The locality is based on the connections of nucleotides given by their phosphodiester and hydrogen bonds. The idea of interpreting secondary structures as chains of structure elements leads us to develop an efficient dynamic programming approach in time O(nm) and space O(nm), where n and m are the lengths of the RNAs. The biological motivation is given by detecting common, local regions of RNAs, although they do not necessarily share global sequential and structural properties. This might happen if RNAs fold into different structures but share a lot of local, stable regions. Here, we illustrate our algorithm on Hepatitis C virus internal ribosome entry sites. Our method is useful for detecting and describing loc...
Sven Siebert, Rolf Backofen
Added 15 Dec 2010
Updated 15 Dec 2010
Type Journal
Year 2007
Where JCB
Authors Sven Siebert, Rolf Backofen
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