The effectiveness of position- and composition-specific gap costs for protein similarity searches
The effectiveness of position- and composition-specific gap costs for protein similarity searches
The flexibility in gap cost enjoyed by Hidden Markov Models (HMMs) is expected to afford them better retrieval accuracy than position-specific scoring matrices (PSSMs). We attempt to quantify the effect of more general gap parameters by separately examining the influence of position- and composition-specific gap scores, as well as by …