[BiO BB] Refined nucleotide BLAST matrix

[Yannick Wurm]

Thank you Peter - what a surprising hack!
Thats the way we'll go.

Thanks again,

-yannick


On 18 févr. 05, at 18:40, Peter Rice wrote:
>> Yannick Wurm wrote:
>>> 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.
>>>
>>> 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.
>>>
>>> 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.
>
> You can get around this - you also need this trick to handle 
> nucleotide ambiguity codes (for example to compare patent sequences 
> which use codes other than 'N'.
>
> You have to cheat though.
>
> 1. Build your blast database as protein
>
> 2. Give your matrix a name that matches one of the blast protein 
> matrix names (!)
>
> 3. Put in the matrix values you want
>
> 4. Remember that you are now using blastp (protein search) so you can 
> only use a short wordsize - I am guessing you have short sequences 
> anyway so this should not be a problem
>
> 5. Remember that BLAST does local alignment.
>
> 6. Remember that your scores will be making some wrong assumptions 
> about using proteins. You should still find the hits you are looking 
> for.
>
> This cheat was published (by NCBI if I recall correctly) some time 
> back. Sorry, I can't track down the reference.
>
> Hope this helps,
>
> Peter Rice

. . . . . . . . . . . . . . . . . .
yannick.wurm at unil.ch
+41.21.692.4157
PhD student, Departement of Ecology and Evolution
Université de Lausanne, Switzerland


. . . . . . . . . . . . . . . . . .
yannick.wurm at unil.ch
+41.21.692.4157
PhD student, Departement of Ecology and Evolution
Université de Lausanne, Switzerland

. . . . . . . . . . . . . . . . . .
yannick.wurm at unil.ch
+41.21.692.4157
PhD student, Departement of Ecology and Evolution
Université de Lausanne, Switzerland

. . . . . . . . . . . . . . . . . .
yannick.wurm at unil.ch
+41.21.692.4157
PhD student, Departement of Ecology and Evolution
Université de Lausanne, Switzerland