[BioPython] qblast

[Michael S. Robeson]

Sure, I am using a really simple script that I wrote (link below) to  
start getting familiar w/ biopython. So, any other comments would be  
greatly appreciated.

http://ucsu.colorado.edu/~robeson/documents/blast.txt

Using this sequence:

TGTGATGGATATCTGCAGAATTCGCCCTTTAAACTTCAGGGTGACCAAAA
AATCAAAATAAATGTTGAAATAATACTGGATCTCCACCACCACTAACTTC
AAAAAATGTTGTATTAAAATTTCTATCAGTTAATAACATTGTTATAGCAC
CCCCTAATACTGGTAATGATAATAATAATAATCATGCTGTTATAAATACA
GCTCAAACAAATAAAGGTAACTTAAACATACTCATACCAGGTGTTCGCAT
ATTAATAACAGTAACAATAAAATTTATTGAACCTAATATTGATGATATAC
CAGCTAAATGTAAACTAAATATTGCACATTCTATTGAACCTCCTGAATGT
GAAAATATACCAGATAATGGTGGATAAACAGTTCAACCTGTACCTGCCCC
CATCTCGACTACAGATGATCAAATTAATAAAAAAAATGATGGTACTAATA
ATCAAAAACTTATATTATTTAATCTTGGGAATGCCATATCAGGAGCTCCT
ATCATTAAAGGTAAAAATCAATTACCAAAACCACCCATTAATGCAGGCAT
AACCATAAAAAATATCATTATTAAAGCATGTGCTGTTATTAACACATTAT
ATGCTTGATGATTGTAATTTAATATTACTGCACCAGCATCTGATAATTCT
ATACGTATTAATATAGATCAAAATGTTCCTATTAAACCTGCTAAAAATGC
AAATATTAAATATAATGTTCCAATATCTTTATGATTTGTTGACCAAGGGC
GAATTCCAGCACACTGGCGGCCGTTACTAG

Using blastn. When I use the web site I set the following:

Database = Others (nr etc..) w/ drop menu set to 'Nucleotide  
collection (nr/nt)'
Optimize for = 'Somewhat similar sequences (blastn)'

I assumed the above was the same as biopython's default qblast when  
using blastn. Basically, my script seemed worked fine until NCBI  
changed the layout of their site (I'd check every so often with a set  
of samples). I also tried to change my code with some of the new  
biopython code. But it is very hard to find good up-to-date  
tutorials. Last time I looked none of them worked.

Anyway, no matter what settings I use via the NCBI web interface I  
cannot get the same results as I do with qblast. So, unless I am  
missing something I wonder if there is something wrong with the back- 
end?

-Mike


On Aug 18, 2007, at 1:25 PM, Peter wrote:

> Michael S. Robeson wrote:
>> I have been using qblast (blastn) for a set of sequences. However,  
>> it  gives me _completely_ different results than if I was to use  
>> the web  interface at NCBI (also using blastn, nr). Is anyone else  
>> having this  problem? Am I missing something?
>
> Could you give us an example? Say three of sequences with details  
> of how you use the web interface, and the code you are using in  
> Biopython.
>
> Peter
>

----------------------------------------------
Michael S. Robeson II
Ecology and Evolutionary Biology
N122 Ramaley Hall
Campus Box 334
University of Colorado
Boulder, CO 80309
robeson at colorado.edu
http://ucsu.colorado.edu/~robeson/