[Biopython] Virus alert during qblast()

[Peter Cock]

Hi again,

Using standalone BLAST+ at the command line with -remote
you can specify an Entrez filter option -entrez_query on the
organism.

Another option which may be better is to make a target
database (e.g all fully sequenced bacteria).

Peter


On Wed, Apr 23, 2014 at 12:45 AM, Michael Fethe <mfethe1 at gmail.com> wrote:
> Hi Peter,
>
> I am blasting unknowns, however, can I limit biopython to bacteria in my qblast command?
>
> Michael Fethe
>
>> On Apr 22, 2014, at 6:02 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>
>> Hi Michael,
>>
>> That seems unlikely - but if you are doing hundreds of
>> automated BLAST queries, the NCBI might not be very
>> happy.
>>
>> For big BLAST jobs, I would always use standalone
>> BLAST running locally (on your cluster if possible).
>> This is generally faster as well :)
>>
>> Regards,
>>
>> Peter
>>
>>> On Tue, Apr 22, 2014 at 10:59 PM, Michael Fethe <mfethe1 at gmail.com> wrote:
>>> Hi,
>>>
>>> I am submitting sequences to blast via biopython. My script
>>> runs over multiple hours and can take quite some time
>>> (working with hundreds of sequences). Is it possible for
>>> my computer or someone to mistake this script running
>>> as a virus since it writes my blast results to an output file
>>> and then submits my next sequence?
>>>
>>> Thanks,
>>>
>>> Michael Fethe
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