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First, let's see how the alignment depends on the choice of substitution matrix. Gap opening penalty equal to 11.
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L would have an average score.
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Mutation data matrix – a scoring matrix compiled based on observation of protein mutation rates: some mutations are observed more often then other (PAM, BLOSUM).
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What special features do these amino acids have? This page titled 9.
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complete the matrix.
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Warning, /data/BLOSUM62 is written in an unsupported language.