[Bioperl-l] EMBL access through bioperl

[govind chandra (JIC)]

Hello,

I would like to know if there is a way to get EMBL files (from EBI or
Heidelberg) similar to the way it is possible to get them from GenBank
(Bio::DB::GenBank). I think I heard some mention of it on this list sometime
back. I have Bioperl 0.7.1 and could not find any module for doing this.

I can get the files from GenBank and write them out as EMBL using Bio::SeqIO
but have noticed that these files have an additional feature called 'gene'
for every CDS (compared with the corresponding embl files got directly from
EMBL). The conversion is perfect, it is just that the GenBank files have
this additional feature called gene for every CDS. My scripts which write
.ace files for reading into ACeDB rely for everything on bioperl and have
been written with the EMBL format in mind. I could always make them ignore
the feature gene but it will be nice if this format conversion could be
avoided entirely.

I will appreciate any help in this regard.

Govind
(Govind Chandra)
ScoDB 
John Innes Centre
Norwich