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

David dgw106 at york.ac.uk
Wed Mar 21 10:13:21 EDT 2007

Dear Lily,

You can download and run BLAST locally to save network traffic, if you 
prefer, especially if you have many queries to run. Binaries are available 
for many platforms at http://www.ncbi.nlm.nih.gov/BLAST/. Of course, you 
need space to store the databases. For example, the non-redundant protein 
sequence database is a few hundred MB I think...

Parsing BLAST XML output (using the option '-m 7' when running BLAST from 
the command line) can be done easily using the NCBIXML module in Biopython.

This method has the feature that you have a static BLAST version and 
database, so allows for reproducibility, which can be viewed as an 
advantage or disadvantage, depending what you want to do.


On Mar 21 2007, lily xue wrote:

>Hello all,
> Would you please tell me whether it is possible for me to write some 
> script (maybe perl script) to call NCBI Blast and get the plain text 
> result from my own computer? Thanks.
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