| Alternate substitution matrices |
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| • | Substitution
matrices are tailored to detecting |
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| similarities
among sequences that are diverged by |
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| differing degrees |
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| • | BLOSUM-62 is
among the best for detecting most |
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| weak protein
similarities |
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| • | Short but strong
alignments are more easily detected |
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| using a matrix
with a higher "relative entropy" |
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