[BioPython] blastn parameters

[Chris Fields]

On Apr 23, 2008, at 3:40 PM, 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

For remote BLAST one should look at the URLAPI parameters instead of  
referring to 'blastall' docs; there are some similarities but I think  
a few parameter defaults are different, just can't remember which ones  
(maybe eval cutoff, default result format display...)

Here's the latest:

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/

chris