Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix.
Jakob Hull HavgaardElfar TorarinssonJan GorodkinPublished in: PLoS Comput. Biol. (2007)
Keyphrases
- pairwise
- matrix representation
- similarity matrix
- sequence alignment
- programming language
- global alignment
- rna sequences
- higher order
- semi supervised
- markov random field
- multiple alignment
- pruning method
- multi class
- loss function
- structural information
- similarity measure
- search space
- spectral clustering
- dissimilarity matrix
- linear algebra
- programming environment
- pruning algorithms
- low rank
- similarity function
- singular value decomposition
- high order
- object oriented programming
- secondary structure
- pruning algorithm
- dynamic programming
- rna secondary structure prediction
- structural features
- rna secondary structures
- proximity matrix
- string kernels
- pairwise constraints
- computer programming
- genome wide
- statistical significance
- recommender systems
- search algorithm