[BiO BB] Problem with BLAST

[Jose Maria Gonzalez Izarzugaza]

The fact is that BLAST counts the percentage of [ATCG] in the query or 
something similar.

You can try a query like that ATATACACATTTGArrrrrrr setting the option 
'Mask lower case' to active.

It works (or seems to)  and returns an aligment for the ATATAT...GA 
zone... by chance???... Maybe. :o(

Good luck!
Txema




Joe Landman wrote:

> Did you mean to translate your nucleotide sequence into a protein 
> sequence?  You would need to use either blastx to do the translation, 
> or one of the tblast series (depending upon what you were searching 
> against).
>
> Balaji 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
>
>
>