[BiO BB] how to visit NCBI Blast and get the plain text result using script

Ann Loraine aloraine at gmail.com
Wed Mar 21 17:31:24 EDT 2007

Speaking of python, does anybody know how to get urllib in python to
send POST data?

I'm used to building URLs and opening them using urllib.urlopen, but
have wondered how to send data via "post" as well as "get." Perhaps
there is a good library available for this, besides urllib? Or maybe
urllib has the ability to do this, and I have not been reading the
docs carefully enough.

A code snippet would be much appreciated!

All the best,


On 3/21/07, Dr. Christoph Gille <christoph.gille at charite.de> wrote:
> I have done this EBI blast and
> I guess that it is also easily possible with NCBI.
> You can get it in computer readable form (XML) or in
> human readable form.
> Your script needs to send the POST data i.e. the
> query sequence and the other settings.
> Check the man pages of wget or w3m for this.
> Depending on your favorite computer language you
> can use tool-kits. They make thinks much more convenient
> for you. I would highly recomend to use one of those.
> Python: Biopython,
> Perl: Bioperl,
> Java: STRAP, Biojava
> Ruby: BioRuby
> Good luck!
> Christoph
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Ann Loraine, Assistant Professor
Departments of Genetics, Biostatistics,
Computer and Information Sciences
Associate Scientist, Comprehensive Cancer Center
University of Alabama at Birmingham

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