[BiO BB] Refined nucleotide BLAST matrix

[Daniel Amelang]

Hi Yannick,

  Forgive me if I misunderstood your question, but I think what you're 
looking for is the '-DNAMATRIX=custom_matrix.mat' option of clustalw. 
I'm using it for a project of mine and it works great. Let me know if 
you need help getting it to work. Sometimes clustalw can be picky about 
the format of the matrix.

Dan Amelang

Yannick Wurm wrote:

> Hi,
> for a specific need in my lab, we are looking for an implementation of 
> nucleotide sequence alignment program which would be more flexible 
> than standard BLAST.
> The reason is that we have sequenced dna fragments which have been 
> submitted to chemical modifications which differentially affects 
> different nucleotides.
>
> To help identify these sequences, we need to be able to fine-tune the 
> matrix used for scoring. Thus, for example when calculating the 
> "score" of an aligment, C->A and C->T could be given different weights.
>
> According to ebi.ac.uk, the WU-blast matrix is:
>          A          T         G        C
>     A    5
>     T   -4         5
>     G   -4        -4         5
>     C   -4        -4        -4        5
>
> We want to be able to specifiy inidividual values to something like 
> the following example:
>          A          T         G        C
>     A    2
>     T   -4         8
>     G   -8        -10        3
>     C   -2        -1        -3        10
>
>
> To my surprise, BLAST does not have this liberty, despite the fact 
> that different scoring matrices are used for proteins. I couldn't find 
> anything on Google either.
>
> Would anyone one the list have a clue? Or do I need to get dirty 
> messing with BLAST's source?
> Thanks in advance,
>
> Yannick
>
> . . . . . . . . . . . . . . . . . .
> yannick.wurm at unil.ch
> +41.21.692.4157
> PhD student, Departement of Ecology and Evolution
> Université de Lausanne, Switzerland
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