Hi Kieren,
unfortunately, its not possible. Two ways of doing this:
1- connect to publicly available mart databases
mysql -uanonymous -hmartdb.ensembl.org -P5316 -A
use sequence_mart_54;
and e.g HUMAN sequences are in table:
hsapiens_genomic_sequence__dna_chunks__main
there is chr_name,chr_start and sequence attributes to retrieve sequence
in chunks.
2- use Ensembl API
Best,
Syed
Kieren Lythgow wrote:
Hi,
Is it possible to retrieve reference sequences using Biomart? In the
Sequence>Attributes section there does not appear to be this option. Options
include coding region, flanking sequence, transcripts etc but no options for the
entire unannotated reference DNA sequence.
Many thanks
Kieren Lythgow
PhD student
Mitochondrial Research Group
Institute of Ageing & Health
Newcastle University
UK
