[BiO BB] Refined nucleotide BLAST matrix

Yannick Wurm idh at poulet.org
Fri Feb 18 09:15:56 EST 2005

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.wurm at unil.ch
PhD student, Departement of Ecology and Evolution
Université de Lausanne, Switzerland

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