HMMSUM (HMMSTR-based SUbstitution matrices) is a new model for structural context-based amino acid substitution probabilities consisting of a set of 281 matrices, each for a different sequence-structure context. HMMSUM does not require the structure of the protein to be known. Instead, predictions of local structure are made using HMMSTR, a hidden Markov model for local structure. Alignments using the HMMSUM matrices compare favorably to alignments carried out using the BLOSUM50 matrix when validated against curated remote homolog alignments from BAliBASE. HMMSUM has been implemented using local Dynamic Programming and with the Bayesian Adaptive alignment method. The download package contains the essential programs from HMMSTR (see above) and the HMMSTR model itself, alng with Smith-Waterman local dynamic programming and Bayesian Adaptive alignment programs, modified to use the HMMSUM matrices.
- Fortran compiler
:: MORE INFORMATION
Huang, Y-M, & Bystroff, C. (2006)
Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions.