[Biococoa-dev] starting BCAlignment

[John Timmer]

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
alignments.

If all of this is correct, then I think I know enough to actually help ;).

JT

_______________________________________________
This mind intentionally left blank