[BiO BB] Problem with BLAST

Marcos Oliveira de Carvalho operon at cbiot.ufrgs.br
Tue Jun 14 11:10:15 EDT 2005

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  

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.



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
> _______________________________________________
> Bioinformatics.Org general forum  -   
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board

More information about the BBB mailing list