Voß, Björn; Giegerich, Robert; Rehmsmeier, Marc: Complete probabilistic analysis of RNA shapes. In: BMC Biology. Jg.4 H. 1. 2006
Inhalt
- Outline of probabilistic shape analysis
- Results
- Modelling the folding space
- Deriving features from structures
- Complete probabilistic shape analysis
- Transfer RNA
- Attenuator
- Leader of ptsGHI
- Precursor of microRNA lin-4
- mRNA
- Approximating shape probabilities via sampling
- Discussion
- Mathematical and algorithmic aspects
- Biological adequacy of shapes
- Significance of predicted structures
- Conclusion
- Methods
- Algorithmics and efficiency analysis
- Notation
- Bellman's Principle
- Definition and justification of objective function h
- Definition and justification of objective function h
- Dynamic programming with classification
- Why probabilistic shape analysis is expensive
- Further implementation details
- A non-ambiguous grammar with correct dangles
- Practical efficiency
- Shape probabilities based on sampling
- Availability and requirements
- Authors' contributions
- Acknowledgements
- References