[BioPython] blastn parameters
Chris Fields
cjfields at uiuc.edu
Wed Apr 23 21:07:44 UTC 2008
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
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