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

Jonathan Miller millerj at bcm.tmc.edu
Mon Apr 4 00:26:49 EDT 2005

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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