[Biopython] Blast.NCBIWWW qblast taxonID search space limitation

[Carlos Javier Borroto]

On Thu, Sep 24, 2009 at 11:34 AM, Michael S. Koeris
<michael.koeris at gmail.com> wrote:
> I saw the option to put in an [ORGANISM] but I was hoping I could use the
> TaxonID because say I want to BLAST all bacteria or all archea
>

I'm just doing exactly that, by putting on my entrez_query something like this:
"txid6945[Organism:noexp]"

I got that string by searching on the taxonomic database and then
clicking to see all of the sequences of that taxon. I haven't tried to
use only "txid6945" don't know what is the meaning of
"[Organism:noexp]", but I can tell you this works.

As a side note on blasting, I think there is a bug on the XML
generator from NCBI, I getting stuff like this:
>>> print blast_record.descriptions[0].title
gi|241564310|ref|XP_002401874.1| E1-E2 ATPase, putative [Ixodes
scapularis] >gi|215501920|gb|EEC11414.1| E1-E2 ATPase, putative
[Ixodes scapularis]

I have to do odd thing like:
>>> print blast_record.descriptions[0].title.rsplit('>')[0]
gi|241564310|ref|XP_002401874.1| E1-E2 ATPase, putative [Ixodes scapularis]

And is not a bug on the biopython parser, cause I see the title is
wrong on the xml output.

Hope its help
-- 
Carlos Javier Borroto
Baltimore, MD
Phone: (410) 929 4020