[BioPython] Human genome

[Frank Kauff]

On Tue, 2005-03-01 at 10:34 +0100, Eirik Sønneland wrote:
> Hi & thanks for replying!
> 
> Yes, I'm aware of the cookbook and the links to NCBI, but it doesn't 
> seem to be any database which is only for human, as there is for 
> forexample "Drosophila genom".
> Interesting aspect that you've changed to standalone blast and that it 
> isn't faster...hmmm,
> 

Standalone blast needs a lot of resources on your local computer, of
which often memory is the bottleneck. Without plenty of memory, blast
can't keep the database in ram and the search takes quite a long time.
The nt database on a local machine with less than a few GB of ram can be
rather stressful for your harddisk. NCBI on the other side can be very
fast, e.g. if you're blasting during the (US) night or early morning. 

Frank

> regards
> Eirik
> 
> DroMartina wrote:
> 
> > Hallo Eirik,
> >
> > have a look at the cookbook:
> > http://www.biopython.org/docs/tutorial/Tutorial004.html#toc10
> >
> > I just tried to do the same, but each query took 1-2min. So I switched 
> > to standalone Blast, but its not faster yet.
> >
> > Martina
> >
> > Eirik Sønneland wrote:
> >
> >> Hi!
> >>
> >> Need to Blast my sequence file against the human genome. Have tried 
> >> to search http://www.ncbi.nlm.nih.gov/BLAST/docs/netblast.html for 
> >> finding this database to put into the following code (as second 
> >> argument):
> >>
> >> NCBIWWW.qblast('blastn', '???', f_record),
> >>
> >> Have anybody knowledge  of the name of this parameter ??
> >>
> >> Would be highly appreciated!
> >>
> >> cheers,
> >> Eirik
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> >
> 
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-- 
Frank Kauff
Dept. of Biology
Duke University
Box 90338
Durham, NC 27708
USA

Phone 919-660-7382
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Web http://www.lutzonilab.net/member/frankkauff.shtml