[Bioperl-l] Standalone blast

[khush ........]

Dear Florent,

Thank you very much for your kind reply and let me clear the concept of
running the blast. I am working with simple machine so I need to take
permission from my administrator to work on some good server to have whole
nr database from NCBI and run the blastx.

Thank you

Kamal
Bioperl is great.


On Fri, Apr 29, 2011 at 10:54 AM, Florent Angly <florent.angly at gmail.com>wrote:

> Hi Kamal,
>
> To run BLAST the way Dave described, you need to have BLAST installed on
> your computer, and you need to download BLAST databases to your computer (or
> make them yourself with the formatdb command). There are plenty of databases
> available on the NCBI FTP website: ftp://ftp.ncbi.nih.gov/. And yes, some
> of these databases are very large and will take a long time to download. By
> the way, the BLAST may also take a very long time to execute if you use
> large databases, so, you'd better run the analysis on a powerful computer or
> a server.
>
> Also read this documentation:
> http://search.cpan.org/~cjfields/BioPerl-1.6.900/Bio/Tools/Run/StandAloneBlast.pm<
> http://search.cpan.org/%7Ecjfields/BioPerl-1.6.900/Bio/Tools/Run/StandAloneBlast.pm
> >
> It stipulates that you can BLAST an entire FASTA file (not just a sequence
> object):
>
>  $inputfilename  =  't/testquery.fa';
>  $blast_report  =  $factory->blastall($inputfilename);
>
>
> Regards,
>
> Florent
>
>
>
>
>
> On 29/04/11 14:53, khush ........ wrote:
>
>> Dear Dave,
>>
>> Thank you for your support.
>>
>> If need to change the following lines like
>>
>> $blast_obj = Bio::Tools::Run::StandAloneBlast->new(-program  =>  'blastx',
>> -database =>  'nr.fa'));
>>
>> $seq_obj = Bio::Seq->new(-id  =>"test query", -seq =>"file.fa");
>>
>> I have a simple and basic query for you, as I am beginners in bioperl,
>> that
>> if I need to download the whole nr database from NCBI to run the code or
>> It
>> will directly fetch information from the NCBI website. I do not understand
>> it, because downloading the whole nr d/b itself takes long time for me.
>>
>> How could I read whole file instead of simple string "TTTATAGATAGAGACAG"
>> in
>> -seq (a fasta file). Is there a simple way to do the exercise according to
>> my conditions.
>>
>> Thank you
>> Kamal
>>
>>
>> On Thu, Apr 28, 2011 at 12:59 PM, Dave Messina<David.Messina at sbc.su.se
>> >wrote:
>>
>>  Hi Kamal,
>>>
>>> This is covered in the beginners' HOWTO:
>>> http://www.bioperl.org/wiki/HOWTO:Beginners#BLAST
>>>
>>>
>>> Dave
>>>
>>>
>>> On Thu, Apr 28, 2011 at 07:22, khush ........<bioinfo.khush at gmail.com
>>> >wrote:
>>>
>>>  Hi,
>>>>
>>>> I have some sequences ~250 and wanted to use BLASTX to blast against nr
>>>> database of NCBI, as this is time consuming using web based search. Can
>>>> some
>>>> one please tell me how to start BIOPERL with scuh problems. I know that
>>>> this
>>>> is possible with bioperl, but do not know how.
>>>>
>>>> Any suggestion will be appreciable.
>>>>
>>>> Thanks in advance
>>>> Kamal
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>>>>
>>>>
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>