[BioPython] blast

[Brad Chapman]

Hi Esra;

> I have written a code for blast but it gives a syntax error as 
> "unexpected end of stream." 
> the code is:
[...]
> query='AC092140'
> b_results = NCBIWWW.blast('blastn', 'human genome', query)

There is nothing wrong with your code in terms of form, but the problem
is the way you are using BLAST. There are really two problems here:

1. You use 'human genome' as the database. There is no database called
this at NCBI. If you look here:

http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html#nucleotide_databases

you can get a list of all databases that are available to use. We only
deal with the "standard" BLAST page, not the specialized genome only
BLAST pages that NCBI has.

To tell this, you can just print out the results from the blast before
putting them into the parser, to look at what you got. You'll see
(cluttered amongst a bunch of HTML):

ERROR: Failure to initialize BLAST database 'human genome'

2. The query sequence AC092140 is an entire YAC clone 193kb in size.
This is way too big for a BLAST query and will take forever to run;
you'll definitely get time-out errors before it can be finished.

Hope this helps.
Brad