Generic Genome Browser (GBrowse) Databases

Solanaceae Comparative Genome Database

This database contains all public genomic contig sequence data for the Solanaceae available from GenBank. Currently, our Solanaceae Comparative Genome Database includes BACs from the Tomato Genome Initiative and the Potato Genome Initiative. We will be updating this database quarterly, and will be adding data from the Tobacco Genome Initaitive once it is released and available in the public sequence databases.

The sequences are run through the MAKER pipeline to provide gene models, in addition to any previously annotated gene models from the public data.

Other data and analyses results available for display include:

• Assembled Solanaceae transcript sequences obtained from PlantGDB (PUTs) aligned to the genomic sequence (11 species)
• UniProt's SwissProt and UniRef protein databases aligned to the genomic sequence
• Top hits for the Solanaceae gene models against model dicot proteomes (Arabidopsis, Grape, Medicago, Poplar)
• InterProScan results on the models
• Predicted repeat features (using RepeatMasker and ssr.pl from Gramene)
• Predicted ncRNA features (using tRNAscan-SE and RNAmmer)
• Results of additional computational analyses

Model Dicot Genome Comparative Databases

Genome databases for the current public releases of model dicot genomes with tracks of data from comparative analyses against Solanaceae sequence.

Arabidopsis Genome Database

TAIR8 release of the Arabidopsis thaliana genome.

Grape Genome Database

Genoscope v1.1 release of the Vitis vinifera genome.

Poplar Genome Database

DOE JGI v2 release of the Populus trichocarpa genome.