[Biopython] Qblast : no hits

[Peter]

On 24 Apr 2010, at 04:27, Karthik Raja <cloudycrimson at gmail.com> wrote:

> Hello Peter,
>
> I did try changing the paramters according to the WWW BLAST and its  
> gives an
> error saying "no RID or no RTOE found". Its the same error i was  
> trying to
> tell you in the 1st post. Its the "request time of execution". Is  
> there any
> way to change this RTOE i.e. to increase it? Any idea?
>
> On Fri, Apr 23, 2010 at 5:30 PM, Chris Fields  
> <cjfields at illinois.edu> wrote:
>
>> On Apr 23, 2010, at 4:49 AM, Peter wrote:
>>
>>>> ...
>>>
>>> Differences between a manual BLAST search on the NCBI website
>>> and a script search via QBLAST are almost always down to different
>>> parameter settings. The NCBI have often adjusted the defaults on
>>> the website, and they no longer match the defaults on QBLAST.
>>> You should check things like the expectation cut off, the matrix,
>>> gap penalties etc. The simplest option would be just to copy the
>>> current defaults from the website into your python code.
>>>
>>> We probably need to put this into the Biopython FAQ ...
>>>
>>> Regards,
>>>
>>> Peter
>>
>> Same for BioPerl.
>>
>> chris
>>
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