[Bioperl-l] Standalone blast

[khush ........]

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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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>