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This matrix is calculated by observing the differences in closely related proteins. The PAM1 matrix is used as the basis for calculating other matrices by assuming that repeated mutations would follow the same pattern as those in the PAM1 matrix, and multiple substitutions can occur at the same site. Using this logic, Dayhoff derived matrices as high as PAM A matrix for more distantly related sequences can be calculated from a matrix for closely related sequences by taking the second matrix to a power.
This is how the PAM matrix is calculated. Dayhoff's methodology of comparing closely related species turned out not to work very well for aligning evolutionarily divergent sequences.
Sequence changes over long evolutionary time scales are not well approximated by compounding small changes that occur over short time scales. Henikoff constructed these matrices using multiple alignments of evolutionarily divergent proteins. The probabilities used in the matrix calculation are computed by looking at "blocks" of conserved sequences found in multiple protein alignments.
These conserved sequences are assumed to be of functional importance within related proteins and will therefore have lower substitution rates than less conserved regions.
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To reduce bias from closely related sequences on substitution rates, segments in a block with a sequence identity above a certain threshold were clustered, reducing the weight of each such cluster Henikoff and Henikoff. One would use a higher numbered BLOSUM matrix for aligning two closely related sequences and a lower number for more divergent sequences.
Many specialized substitution matrices have been developed that describe the amino acid substitution rates in specific structural or sequence contexts, such as in transmembrane alpha helices,  for combinations of secondary structure states and solvent accessibility states,    or for local sequence-structure contexts.
Share Give access Share full text access. Share full text access. Please review our Terms and Conditions of Use and check box below to share full-text version of article. Abstract This article examines the effects of exchange rate alignment during — on agricultural producer support estimates PSEs for India. Citing Literature. Volume 36 , Issue 2 March Pages Related Information. Close Figure Viewer.
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