[BioPython] qblast
Peter
biopython at maubp.freeserve.co.uk
Sat Aug 18 21:47:31 UTC 2007
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
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