[Bioperl-l] your kind help needed!

[xiefuliang]

Hello, dear administrators.

 

I am fresh man for bioperl. At present, I find the efficiency is very high with bioperl. So, I want to thank the people who contribute to Bioperl, you too. 

 

Now, I have some question in using bioperl. As listed below:

1. Sequence Retrieval from Local Database

 

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

I hope you can test the module again. Thanks.

 

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.



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? 

 

Thank you for your help.

 

Regards,

 

 

Xie Fuliang