Optimizing amino acid substitution matrices with a local alignment kernel.
Hiroto SaigoJean-Philippe VertTatsuya AkutsuPublished in: BMC Bioinform. (2006)
Keyphrases
- amino acids
- sequence alignment
- protein sequences
- positive definite
- biological sequences
- positive semidefinite
- protein function
- kernel function
- protein structure prediction
- secondary structure
- protein classification
- kernel methods
- support vector
- physico chemical
- amino acid sequences
- sequence databases
- protein structure
- computational biology
- protein folding
- feature space
- kernel matrix
- smith waterman
- physicochemical properties
- psi blast
- tertiary structure
- pairwise
- component analysis
- protein families
- contact map
- dynamic programming
- prediction accuracy
- fine grained
- string kernels
- social networks