Janssen, Stefan ; Giegerich, Robert: Ambivalent covariance models. In: BMC Bioinformatics. Jg.16 H. 1. 2015
Inhalt
- Allowing for structural variation in RNA families
- Introduction: classical covariance models
- Recreating the core of Infernal
- Overview
- ADP and the Bellman's GAP system
- Change 1: replacing the architecture grammar
- Change 2: gaining posteriors
- Approving faithful re-implementation
- Ambivalent covariance models
- Problem definition and input format
- Overview of the aCM generation process
- Check for compatibility of consensus structures
- Parsing individual guide trees
- Ambivalent guide forest
- Provide indices in the ambivalent guide forest
- Generate aCM grammar
- Evaluation
- The tRNA family as an aCM
- U5 spliceosomal RNA as an aCM
- Merging RNAse-P RNA families
- Merging IRES families
- Conclusion
- Additional file
- Competing interests
- Authors' contributions
- Acknowledgements
- References