D grimshawi project
This page should be used to add any useful tidbits or helpful advice anyone finds that is specific to the D grimshawi finishing and annotation project.
Early work on the Agencourt assemblies of the D. grimshawi genome identified two scaffolds as being likely derived from the dot chromosome. Both of these scaffolds contain a high density of putative orthologs of D. melanogaster dot chromosome genes.
These scaffolds were analyzed and the list of all fosmids mapping to these scaffolds was extracted. This list was cross-referenced to the list of clones available for order from the Drosophila Genome Resource Center. The available fosmids that mapped to the two scaffolds were analyzed and a set of overlapping fosmids were ordered. However, not all fosmids were viable and only 40 fosmids were returned. This set of fosmids covers about 85% of the two scaffolds. Unfortunately about 15% of the scaffolds were not covered by any available clones.
Viewing the Two Scaffolds in Genome Browsers
You can view the two grimshawi contigs in their entirety on either the UCSC browser or the flybase browser.
However you should be aware that the two browsers are using slightly different assemblies.
The UCSC browser is displaying the original Agencourt Arachne assembly while the flybase browser displays the CAF-1 assembly in which minor updates have been made to reconcile the results of various assembly programs. The consequences of the CAF-1 update is that the same regions of the dot chromosome from grimshawi do not have the same scaffold numbers and the coordinates no longer match precisely. You can use the the links below to view these regions (the UCSC version has the locations of the fosmids mapped onto the scaffolds, the flybase version does not):
Warning! the locations of the fosmids on the UCSC browser are only approximate; to find the exact location of any fosmid on this browser a BLAT search with end sequences should be carried out.
The 41 fosmids have been duplicated with slightly different names to facility data tracking. Now each project name will only be sent out once but each fosmid will have two names. The table below cross-references the name of the fosmid in the CAF1 assembly with the two names it has within the GEP system.
|original name||GEP name 1||GEP name 2|