[BioPython] qblast
Michael S. Robeson
Michael.Robeson at Colorado.EDU
Sat Aug 18 16:51:24 EDT 2007
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/
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