Fwd: [Biococoa-dev] starting BCAlignment
biococoa at bioworxx.com
Wed Mar 9 14:59:58 EST 2005
> Am 09.03.2005 um 20:45 schrieb John Timmer:
>> Just so I have this straight -
>> Google tells me that the substitution matrix is just a way to look up
>> score that indicates how good an alignment between two amino acids is.
> A T G C
> A 9 3 2 1
> T 3 9 3 2
> G 2 3 9 1
> C 1 2 1 9
> for a dna sequence matrix. As you can see, every matrix has to be
>> 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
> Thats the point.
>> The matrix is simply something that researchers have devised, and not
>> inherent property - different matrixes exist, and may produce
> yes there are special matrices for special purposes. For example you
> can define a matrix to align specific domains better and so on.
>> If all of this is correct, then I think I know enough to actually
>> help ;).
> you are completly right !!! :-)
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