Ensembl

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Ensembl is a joint project to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes.

[edit] Fetching sequences

I found this thread very informative. --Jhannah 08:45, 25 January 2008 (CST) 

I don't think there's a direct BioPerl interface to Ensembl, but BioMart at
Ensembl itself will get you sequences (and lots of other things if you want)
given a list of Ensembl IDs.

http://www.ensembl.org/biomart/martview 

If you want to be able to get Ensembl sequences from a program, there's the
Ensembl API:

http://www.ensembl.org/info/using/api/core/core_tutorial.html

Various approaches are discussed here:

http://www.bioperl.org/wiki/Getting_Genomic_Sequences 

Since you have ENSEMBL ids I'd think that would be the way to go.
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