[Bioperl-l] your kind help needed!

Sendu Bala bix at sendu.me.uk
Wed Jan 31 09:36:18 EST 2007


xiefuliang wrote:
> 
> use Bio::DB::Fasta;
> 
> my $db = Bio::DB::Fasta->new($dir_with_fa_files);
> 
> my $seqstr = $db->seq(‘SEQUENCE1’);
> 
> When I used the module, I found  $db->seq(‘SEQUENCE1’) will retrieve
> the corresponding sequence and the ID of next sequence.
> 
> e.g.  The result is
> 
> AGCTTGGGGAAGGTT
> 
>> DFOOO1

This may be due to your old version of Bioperl, but if not, post the
file that contains SEQUENCE1 (if it is reasonably small).


> 2. I want to make BLASTX in GenBank, swissprot, or other protein
> databases. And I just want to obtain the best hit information (HSP).
> I found several modules can do the work. But I do not know which one
> is the best. I failed to obtain the best hit information. If
> conveniently, could you send me some example source code, which
> including how to make BLASTX and obtain the best hit  information.

See the SearchIO HOWTO:
http://www.bioperl.org/wiki/HOWTO:SearchIO


> 3. I use the command line ‘ppm install bioperl’ to install bioperl.
> So, I have only bioperl 1.2 in computer. How can I update my bioperl?

Install Bioperl 1.5.2:
http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows


Hope that helps,
Sendu.


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