Arabidopsis thaliana gene models can often be improved and expanded by taking into account EST and cDNA evidence-based alignment. AtGDB facilitates the curation and correction of gene models through Community Annotation. Our system consists of the online annotation tool yrGATE (see below left), plus tables showing gene models most in need of improvement (below right).

Community Annotation Using yrGATE

The yrGATE (Your Genome Annotation Tool for Eukaryotes) is an online tool for inspecting and correcting erroneous gene models, based on evidence alignment data (cDNA, EST, protein). Any registered user can create a Community Annotation account and learn to annotate genes. Visit Annotation Central to view previous users' annotations, or create a new account and start adding your own!

Example of a yrGATE Annotation

UCA-At2g42245:
The User Contributed Annotation (green gene structure) to the left shows how a user of AtGDB has provided an updated annotation. This annotation explains the inconsistancy of the current gene models with the spliced alignment of ESTs and cDNAs in this region.

GAEVAL (Genome Annotation EVALuation) Tables

The GAEVAL system identifies potentially erroneous gene models, based on conflicts with evidence alignments (cDNAs, EST, proteins). The results are presented in tabular form with links to the yrGATE community annotation tool, so users can rapidly identify genes in need of annotation. See link below for AtGDB GAEVAL table. More...

GAEVAL Categories and Totals for AtGDB (with links to GAEVAL Help Page descriptions)

Type	Description	Count
Alternative Splicing	Splicing pattern different from the one specified by gene model	45,000
Alternative Transcript Termination	Evidence transcripts differ in 3' end	65,000
Gene Fission	Two gene models appear to refer to the same transcript	65,000
Gene Fusion	A single gene model appears to refer to two or more distinct transcripts	65,000
Erroneous Gene Overlap	Overlap is not supported by transcript evidence	65,000

Tutorials

If you are a beginning annotator, check out our tutorials which take you throught the annnotation process step by step. Our Annotation Guide provides comprehensive information about the annotation tools and methodologies at PlantGDB.

Community Annotation resources

Other projects related to Community Annotation.

Internships & Outreach

References

Wilkerson, M.D., Schlueter, S.D. & Brendel, V. (2006) yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes. Genome Biol. 7, R58. [PubMed ID: 16859520]
Schlueter, S.D., Wilkerson, M.D., Huala, E., Rhee, S.Y. & Brendel, V. (2005) Community-based gene structure annotation for the Arabidopsis thaliana genome. Trends Plant Sci. 10, 9-14. [PubMed ID: 15642518]

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Community Annotation - Overview