DroSpeGe About Arthropods BLAST BioMart Maps Data News
Ref: Bionet.biology.computational

modENCODE plus Twelve Genomes of Drosophila

Don Gilbert gilbertd at bio.indiana.edu
Tue Mar 21, 2006

2008 Sept. update: Drosophila melanogaster Transcriptome expression
including gene predictions, a big map of the genome with expression, and more

Dear colleagues,

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 gilbertd@indiana.edu

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 http://insects.eugenes.org/DroSpeGe

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 proteomes. See http://insects.eugenes.org/species/news/genome-summaries/

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. See http://insects.eugenes.org/species/maps/muller-elements/

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 downloading.

Don Gilbert, March 2006

Developed at the Genome Informatics Lab of Indiana University Biology Department