Biases in Amino Acid Replacement Matrices and Alignment Scores Due to Rate Heterogeniety


Empirically derived amino acid replacement matrices are widely used in sequence comparison and database searches. We consider an extension of the usual Markov process model of protein evolution that admits site to site rate heterogeneity and demonstrates that rate heterogeneity can introduce a bias in estimated replacement probabilities and the… (More)
DOI: 10.1089/cmb.1996.3.307

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