added 6 genome-wide promoter collections
COTRASIF
+ added 75 Gasterosteus aculeatus (stickleback) promoters
+ added 973 Macaca mulatta (rhesus) promoters
+ added 106 Monodelphis domestica (opossum) promoters
+ added 4 Ornithorhynchus anatinus (platypus) promoters
+ added 466 Oryzias latipes (medaka) promoters
(For all of these species, low number of imported promoters is the
consequence of most genes being not mapped to chromosomes.)
These are the last species in Ensembl which match COTRASIF's import
rules: all the other Ensembl species do not have any exposed values
for the Chromosome filter (that is, genes are not yet mapped). To
verify, an attempt to import "Gorilla gorilla" promoters led to a file
full of "Sequence unavailable" messages; it is likely that all the
other species will produce similar results.
This import brings the total number of genome-wide promoter
collections available for search in COTRASIF to 20.
As the number of promoters per species varies greatly, we'll be adding
the Statistics page soon - to clarify the status of each promoter
collection and orthology mappings.
We are also looking into adding other sources to the COTRASIF's import
pipeline. So far the most probable candidate is the GRAMENE dataset of
the CSHL, which is also available via www.biomart.org and seems to
follow Ensembl-like dataset structure.
Other suggestions are welcome.
COTRASIF team