The new modENCODE project
will be a boon to model organism functional genome data, and I'd like
to join with others in collaborating or consulting on the data
coordination center planned for this research network.
This would be in my view an excellent way to prove and improve the
computational tools of GMOD's Generic Model Organism Database
framework, as well as build a fully operational data center for large
scale functional elements in C. elegans and/or D. melanogaster.
If interested, please contact me at firstname.lastname@example.org
Here is an update also on my recent contributions to MOD and GMOD
usage. Twelve genomes of Drosophila species, from D.ananassae to D.
willistoni and D. yakuba, containing over 2 Billion nucleotides, are
available to genome browsers, grazers and gulpers at
Additions over the last month include D. willistoni, the largest
genome, and updates to D. yakuba and others of this comparative
annotation freeze 1 collection of genomes.
Genome sizes range from 140 megabases for D. melanogaster to over 230
megabases for D. ananassae and D. willistoni. Genome summaries
include sizes, D.melanogaster DNA coverage in species, matches
to D. melanogaster genes, and matches to eukaryote model organism
Common Chromosomes provide maps with a visual overview of Muller's
elements and large scale synteny among these genomes. The close
melanogaster relatives D. simulans and D. yakuba are nearly fully
assembled to five major Muller chromosome elements (A-E) known in the
Drosophila. The more distant D. mojavensis is also nearly fully
assembled, with four chromosome elements (B,C,D,E) larger than D.
melanogaster equivalents, and the A (sex-chromosome) split among one
major and 3 minor scaffolds.
GMOD's GBrowse Genome maps include D. melanogaster genome DNA
homology, homologies to nine eukaryote proteomes, gene predictions,
marker genes and Drosophila microsatellites. Genome assemblies can be
with NCBI BLAST, with links to genome maps. GMOD/EnsEMBL BioMart
provides data mining access for all these annotations. Annotation data
are available in Gene Finding Format (GFF) and FastA sequence for