[BiO BB] Problem with BLAST

[Marcos Oliveira de Carvalho]

I think that you hit a bug of BLAST(p). Either the manual or "blastall" do  
not show a way to deal with that problem. Maybe the way BLAST know if the  
sequence is protein or DNA is hardcoded, like clustal (using the symbol  
frequencies).

One trick could be change the symbols of your protein (A by W, G by L,  
...) and modify the score matrix you are using accordingly.

cheers

Marcos



On Tue, 14 Jun 2005 11:02:35 -0300, Balaji <p.balaji at gmail.com> wrote:

> Hi everyone,
>    I have a protein that comprises only of Alanine(A), Glycine(G),
> Cysteine(C) and Threonine(T). When i try to use NCBI BLAST with this
> protein, the blast program returns an error saying that the entered
> sequence is a nucleotide (as it evidently has only A's, T's, C's and
> G's) and not a protein sequence.
>    Is there anyway i work around the problem? I'll be grateful for any  
> help
> Thanks in advance
> Balaji
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