[ensembl-dev] Genomic Sequence

Nick Fankhauser lists at nyk.ch
Tue Feb 21 12:44:48 GMT 2012


I want to fetch the gnomic sequence of genes as reference for aligning
sequencing reads. I'm using the following method:

my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
my $gene=$gene_adaptor->fetch_by_display_label($gene_symbol);
my $seq = $gene->slice->seq();

Now this retrieved a sequence of length 81195211 bp for TP53 as
gene_symbol, but the genomic size of that gene should be 19143 bp.

Is there anything wrong with this method and how could it be improved?


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