[Biococoa-dev] starting BCAlignment

John Timmer 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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