[Biopython] qBlast Error and Entrez module

[Peter]

On Mon, Aug 10, 2009 at 3:31 PM, Rodrigo
faccioli<rodrigo_faccioli at uol.com.br> wrote:
> Hello,
>
> I've tried to execute a blast from NCBI. In this way, I'm using the NCBI
> module from Biopython. I read the Biopython Tutorial its Chapter 7. So, my
> code is below.
>
>        result_handle = NCBIWWW.qblast("blastn", "nr",
> "TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN")
>        blast_results = result_handle.read()
>        save_file = open( "1CRN_Blast.xml", "w")
>        save_file.write(blast_results)
>        save_file.close()
>
> However, when I execute this code, I receive the error message: raise
> ValueError("No RID and no RTOE found in the 'please wait' page."
>
> I don't know what I'm doing wrong. So, if somebody can help me, I thank.

I don't see anything wrong with that line, but it isn't working for me either.
Odd. Perhaps the NCBI have changed something... I'll get back to you.

> I have on more doubt about Entrez module. What is the difference between
> Entrez and NCBI ?

The NCBI is the (American) National Center for Biotechnology Information.
They provide lots of online tools including Entrez and BLAST:
http://blast.ncbi.nlm.nih.gov/Blast.cgi
http://www.ncbi.nlm.nih.gov/sites/entrez

> With Entrez module can I execute a protein aligment? If
> yes, could somebody inform a example for me.

No, you can't run BLAST via Entrez. Entrez is like a way to search and
download data from the NCBI.

Peter