Hi Rochak,
Rochak Neupane wrote:
When querying for sequences on a dataset set, without any filters (so as
to grab complete set of sequences), marts seem to be quite slow. Pulling
peptides for human, for example, took an excess of 7 minutes from
ensembl mart. Grabbing peptide sequences from Caenorhabditis elegans
(wormbase db, gene dataset from biomart.org <http://biomart.org>) also
took about 7 or so minutes for a file that turns out to be 9MB.
Our own mart is quite slow when querying a complete set of sequences
from an organism. Is it typical for biomart to take 7-8minutes + when
querying for whole genome sequences?
a- are you using GenomicSequence to retrieve sequences ?
b- do you have ORDER BY property set on sequence exportables (if 'a' is
true). Setting ORDER BY slows down the response considerably and its
only required to cope with inconsistencies in the row order that should
really be fixed on the mart (database) construction level.
Best,
Syed
Thanks,
rochak
