Substitution matrices are used to score aligned positions in a sequence alignment procedure, usually of amino acids or nucleotide sequences.
Two commonly used matrices: PAM and BLOSUM
Two commonly used matrices: PAM and BLOSUM
- PAM = Percent Accepted Mutations (Margaret Dayhoff)
- BLOSUM = Blocks Substitution Matrix (Steven and Henikoff)
PAM VS BLOSUM
PAM
|
BLOSUM
|
| PAM matrices are used to score alignments between closely related protein sequences. | BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences. |
| Based on global alignments | Based on local alignments |
| Alignments have high similarity than BLOSUM alignments | Alignments have low similarity than PAM alignments |
| Mutations in global alignments are vey significant | based on highly conserved stretches of alignments |
| Higher numbers in the PAM matrix naming denotes greater evolutionary distance | Higher numbers in the BLOSUM matrix naming denotes higher sequence similarity and smaller evolutionary distance |
| Example: PAM 250 is used for more distant sequences than PAM 120 | Example: BLOSUM 80is used for closely related sequences than BLOSUM 62 |
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