[BioPython] blastn parameters

[Stefanie Lück]

Thanks for all the reply!
Could someone tell me also  how I can change the paramters over Biopyton? I 
this possible?

Stefanie



----- Original Message ----- 
From: "Bruce Southey" <bsouthey at gmail.com>
To: "Sebastian Bassi" <sbassi at gmail.com>
Cc: "Biopython List" <biopython at lists.open-bio.org>
Sent: Wednesday, April 23, 2008 11:31 PM
Subject: Re: [BioPython] blastn parameters


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
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