PlantGDB Web Browser Support

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Latest update: August 23, 2010

GenBank Release 179 (8-23)

GenBank Release 179.0 sequence data (close date 8-14-2010) are now being downloaded and parsed at PlantGDB. We expect the 179 version update, including updated PUT assemblies, to be complete by mid-September (August 23, 2010).

CpGAT reports exon origins (8-19)

The CpGAT* tool for automated, real-time gene structure annotation now reports the details of each exon origin (whether evidence ID, pasa assembly, or ab inito-derived) in the GFF3 output file. Access CpGAT from any PlantGDB genome browser.
*Comprehensive plant Gene Annotation Tool, release 1.05

Community Annotation Features (8-5)

We have updated the yrGATE tool and the CommunityCentral database for commmunity annotation. Changes include a more consistent annotation naming scheme, and easier to navigate annotation tables. PLEASE NOTE that if you have previously annotated genes, the ID has been changed; the former ID is now part of the Description field and can be retrieved using Search. The Community Annotation system is available for all genome browsers at PlantGDB.

New AcDs Tagging Data (8-3)

AcDs Tagging insertion data for maize have been updated to include redundancy information, confirmation data and southern blot and ipcr images. See example of a Ds Insertion Line

Maize RefGen_v2 genome browser

The revised pseudomolecule assembly of maize inbred B73 (RefGen_V2) was released on March 5, 2010 by the Arizona Genomics Institute. We are busy running spliced-alignment to maize EST, cDNA, PUT, and related-species protein in anticipation of releasing a new version of ZmGDB (expected May, 2010)

Manihot esculenta (cassava) genome browser

The recently-released Manihot esculenta draft genome consists of 11,243 scaffolds spanning 416Mb. PlantGDB will release a cassava genome browser incorporating EST, cDNA, PUT and related-species protein alignments as well as published gene models (expected June, 2010).

Prunus persica (peach) genome browser

The recently-released Prunus persica draft genome consists of 8 pseudomolecules (scaffolds) and an additional 194 nonlinked scaffolds spanning 227.3 Mb. PlantGDB will release a peach genome browser incorporating EST, cDNA, PUT and related-species protein alignments as well as published gene models (expected June, 2010).