[BioPython] qblast

[Peter]

Peter wrote:
> I switched to using plain text output as its easier to read by hand.
> 
> Both correctly understood the input query was 780 letters long.
> Both claimed to be output from BLASTN 2.2.17
> Both claimed to be output from the same database
> 
> There where some differences in the parameters footer - but I'm not sure 
> why.  Using the script:
> 
>   Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, 
> GSS,environmental
> samples or phase 0, 1 or 2 HTGS sequences)
>     Posted date:  Aug 16, 2007  6:06 PM
>   Number of letters in database: -51,729,944
>   Number of sequences in database:  5,751,035
> Lambda     K      H
>     1.37    0.711     1.31
> Gapped
> Lambda     K      H
>     1.37    0.711     1.31
> Matrix: blastn matrix:1 -3
> Gap Penalties: Existence: 5, Extension: 2
> ...
> 
> While using the web browser:
> 
>   Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, 
> GSS,environmental
> samples or phase 0, 1 or 2 HTGS sequences)
>     Posted date:  Aug 16, 2007  6:06 PM
>   Number of letters in database: -51,729,944
>   Number of sequences in database:  5,751,035
> Lambda     K      H
>    0.634    0.408    0.912
> Gapped
> Lambda     K      H
>    0.634    0.408    0.912
> Matrix: blastn matrix:2 -3
> Gap Penalties: Existence: 5, Extension: 2
> ...

Solved: Using qblast in a script defaulted to blastn matrix:1 -3, while 
the new webpage instead defaults to blastn matrix:2 -3

You can check this (and change it) on the webpage by clicking on 
"Algorithm parameters" and under "Scoring Parameters" changing 
"Match/Mismatch Scores" from "2, -3" to "1, -3".

Then the results seem to agree. Does that work for you?

Peter