[BiO BB] Refined nucleotide BLAST matrix
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
The reason is that we have sequenced dna fragments which have been
submitted to chemical modifications which differentially affects
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
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
A T G C
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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