[Bioperl-l] Question regarding BioPerl / BioSQL - InterPro Optional IDs

John LaCava lacava at gmail.com
Fri Jul 3 14:07:50 EDT 2009

Hi all,

I am trying to use the BioPerl-db script:

load_seqdatabase.pl to parse a SwissProt.dat file (Yeast.dat, this is  
the yeast proteome with annotations etc.).

The particular entry I am interested is the InterPro optional ID,  
which is the domain name.

I have put a short stub up which displays the 4 pieces of info I want  
to parse into my data base.
That can be found here:


You can see that near the bottom, we get the optional ID:
$protein_ids->{interpro_domain} = $dblink->{optional_id};

I do not think the bioperl script load_seqdatabase.pl retrieves this  
information.  At least, I cannot find it in the db built from parsing  
a test .dat file.
I would like some help figuring out:
1) WHY doesn't it retrieve this information, since it seems to be  
parsing "all" annotations...
2) HOW might I edit the script to include this particular annotation  
of interest in the info it passes to my db (biosql)

I am a bit out of my depth on this, and so, any help is appreciated.


More information about the Bioperl-l mailing list