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) 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? Thanks, rochak
