[Biopython-dev] Possible problem with NCBIStandalone.blastall

[Sebastian Bassi]

On Fri, Nov 7, 2008 at 8:13 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> -q -5 =>nuc_mismatch = -5 (or as a string)
> -G 3 => gap_open = 3 (or as a string)
> -E 3 => gap_extend = 3 (or as a string)
> -F "m D" => filter="m D" (MISSING!)

I will try with this.

> -e 700 => expectation=700 (or as a string)
> -Y = 1.75e12 => search_length = '1.75e12' (or as a float)

I used string since I have the biopython version with the bug that
doesn't allow me to enter non iterable values.

> the difference.  Its probably due to omitting the filter option (-F).
> If that doesn't resolve the difference then there is something very
> strange going on...

OK, I will check it and get back with the results.
Thank you.
Best,
SB.