Minisymposium 23: Genome Annotation
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M2301: The TIGR Rice Genome Annotation Database
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Presenter: |
Campbell, Matthew A Contact Presenter |
Authors | Campbell, Matthew A (A) Ouyang, Shu (A) Zhu, Wei (A) Lin, haining (A) Hamilton, John (A) Lee, Yuandan (A) Malek, Renae L. (A) Zheng, Li (A) Orvis, Joshua (A) Haas, Brian (A) Wortman, Jennifer (A) Buell, C. R. (A) | | Affiliations: |
(A): The Institute for Genomic Research
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We have been funded by the National Science Foundation to annotate the rice genome and provide access to the annotated genome for the community. We have created a rice annotation database using Sybase called Osa1 that houses sequence and annotation information. We released
version 4 of our rice genome annotation in early January that includes a number of updates and improvements. We have constructed pseudomolecules of the 12 rice chromosomes that represent ~95% of the total genome. We have created gene models using a combiniation of ab initio gene finders and experimental evidence. We have incorporated full length cDNA and EST evidence into gene models and improved our functional assignments. We have performed a comprehensive analysis of alternative splicing in rice and compared it with the data for Arabidopsis. We have generated a series of other annotations for the rice genome including gene ontology assignments, domains, motifs, alignments with flanking sequence tags, and a variety of expression data. We have also developed a series of alignments with other plant species including alignments with ESTs and with genetic markers from wheat, maize and sorghum. The annotation is available to the community through the TIGR Rice Genome Annotation website (http://rice.tigr.org) where the annotation can be viewed in the Rice Genome Browser or downloaded using the Data Extractor Tool. We are currently implementing a Community Annotation tool which allows community experts to refine the structural and functional annotation of our gene models.
