Fwd: [Biococoa-dev] starting BCAlignment

[Philipp Seibel]

>

> 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 
>> a
>> 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 
> symmetric.
>
>>  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.
>
> Thats the point.
>
>> The matrix is simply something that researchers have devised, and not 
>> an
>> inherent property - different matrixes exist, and may produce 
>> different
>> alignments.
>
> 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 !!! :-)