Efficient algorithms for probing the RNA mutation landscape.

ABSTRACT: The diversity and importance of the role played by RNAs in the regulation and development of the cell are now well-known and well-documented. This broad range of functions is achieved through specific structures that have been (presumably) optimized through evolution. State-of-the-art methods, such as McCaskill's algorithm, use a statistical mechanics framework based on the computation of the partition function over the canonical ensemble of all possible secondary structures on a given sequence. Although secondary structure predictions from thermodynamics-based algorithms are not as accurate as methods employing comparative genomics, the former methods are the only available tools to investigate novel RNAs, such as the many RNAs of unknown function recently reported by the ENCODE consortiu

SUBMITTER: Waldispuhl J 

PROVIDER: S-EPMC2475669 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature