[BiO BB] Refined nucleotide BLAST matrix

Yannick Wurm idh at poulet.org
Fri Feb 18 12:33:05 EST 2005

Thanks for your feedback Dan,

I guess that could be what I'm looking for. However, I don't want 
multiple alignments so I don't think clustal will do the trick. 
Basically, I have one interesting sequence for which I would love to 
find a homologue in the Honey bee or Drosophila genome. A standard 
BLAST does not show a significant homology.

My fragment was submitted to chemical treatment which replaces As by 
Cs. My sequence thus has many Cs, some of which were already C in the 
original sequence, some of which were As. This makes finding a perfect 
alignment difficult. So when scoring the "distance" between my sequence 
and a sequence from a genome database, I would like to have a lower 
penalty for A-C than for T-C.

Doing this should increase my chance of finding a homologue.


On 18 févr. 05, at 18:05, Daniel Amelang wrote:

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

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