Substitution matrix

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Substitution matrix

PAM-n
- Build by global alignment
- Comparisons of sequences with no more than n% diversity
- Based on closely related proteins
- n : divergence
 
BLOSUM-n
-  Build by Local alignment
-  Comparisons of sequences with no less than n% diversity
-  Based on observed alignment
-  n : identity

*Practical point:

If you think the alignment is too strict to mismatches, you can use BLOSUM (small value) or PAM (big value) matrix.

*Favorites in the field: BLOSUM62 and PAM250

*WUBLASTN scoring scheme: match (+5), mismatch (-4) -> optimal for detecting homologous DNA alignment that are 65 % identical

*NCBI BLASTN scoring scheme: match (+1), mismatch (-2) -> optimal for detecting homologous DNA alignment that are 95% identical

ref)Sean R.E., 22(8), 2004, nature biotechnology

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