[BiO BB] Refined nucleotide BLAST matrix
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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