Constraints
| Hi-index | 0.00 |
Hidden Markov models of protein domain families are very powerful descriptions for use in protein database searches. The ability of these models to incorporate position-specific insertion and deletion probabilities as well as position-specific amino-acid substitution information gives more detail than non-position-specific methods such as Smith-Waterman or BLAST which are based on standard amino-acid substitution matrices. The drawback for protein database search is that database scoring using dynamic programming and HMM parameters is quite slow, especially when compared to using a protein domain consensus sequence in BLAST. This work proposes a method to search for protein domain family homologs using HMM parameters where the search employs genetic algorithms rather than dynamic programming.