[BioPython] blastn parameters

[Bruce Southey]

Sebastian Bassi wrote:
> On Wed, Apr 23, 2008 at 9:49 AM, Stefanie Lück <lueck at ipk-gatersleben.de> wrote:
>   
>> Hello!
>>  Does anyone knows whether the parameters of NCBI's online blastn (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&MEGABLAST=on&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on)
>>  are the same, when I use blastall for a local blastn (without to change anything)?
>>
>>  On the homepage I couldn't find the parameters.
>>     
>
> Just run the BLAST and the see the parameters at the end of the result page.
> But, now I see there is a place to see parameters, at the end of the
> page, look at this screenshot:
> http://bayimg.com/FaJnAAABH
>
>
>   
Hi,
Well, it really depends...

The NCBI site does track your preferences so if you modify an option it 
will use that value in the future.

It may also depend on which blast version. From the NCBI FAQ, "match 
reward (-r) and mismatch penalty (-q) settings are now 2, -3 (from 1, 
-3)". This is different than blastall version 2.2.17 that I have (could 
be changed in 2.2.18). Word size appears to be another change.

Bruce