[Bioperl-l] Bio::Index:EMBL on embl flatfiles

Brian Osborne brian_osborne at cognia.com
Mon Apr 4 13:45:38 EDT 2005


Is there some identifier in common between the fasta entries and the EMBL
entries? If so what you want to be able to do is to create your EMBL indices
based on this key, but the current Bio::Index::EMBL doesn't do this. If you
want to wait a couple of days I can modify EMBL.pm so it can create this
sort of custom index, or you can try to modify EMBL.pm yourself. If you look
at its sister, Genbank.pm, you'll see that the modifications are not

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Jonathan
Sent: Monday, April 04, 2005 12:27 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Bio::Index:EMBL on embl flatfiles

I have the following task to perform in large
quantities. I can do it successfully with
files from ncbi, in fasta and genbank format.

For various reasons, I would prefer to do it
with embl format annotation files, rather than

I first used formatdb to create a blast index
for Apis_mellifera.AMEL1.1.mar.dna.contig.fa  .

I blast my sequence against this file,
and obtain the expected hit, and then I want to find
annotation for this hit, in embl format
flatfiles (Apis_mellifera.0.dat, etc.) with bioperl.

To do this, I have to first make an index with
bioperl, using Bio::Index::EMBL .

Then I need to use "fetch" within bioperl.
The problem is, that "fetch" within bioperl
doesn't seem to know how to use the fasta
headers to find the sequence in the embl flatfile.

There is probably a simple solution to this
that everyone working with bioperl and embl
flatfiles knows, but I don't know what it

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