[Biococoa-dev] starting BCAlignment
jtimmer at bellatlantic.net
Wed Mar 9 14:45:55 EST 2005
Just so I have this straight -
Google tells me that the substitution matrix is just a way to look up a
score that indicates how good an alignment between two amino acids is. If
it's something rare, like W, a W-W match gets a high score. If it's
something like alanine, it A-A matches get a lower score. If it's not a
match, the score is calculated based on how similar the amino acids are.
The matrix is simply something that researchers have devised, and not an
inherent property - different matrixes exist, and may produce different
If all of this is correct, then I think I know enough to actually help ;).
This mind intentionally left blank
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