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Nucleic Acids Research Advance Access published online on December 1, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl976
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© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

The TIGR Rice Genome Annotation Resource: improvements and new features

Shu Ouyang, Wei Zhu, John Hamilton, Haining Lin, Matthew Campbell, Kevin Childs, Françoise Thibaud-Nissen, Renae L. Malek, Yuandan Lee, Li Zheng, Joshua Orvis, Brian Haas, Jennifer Wortman and C. Robin Buell*

The Institute for Genomic Research, 9712 Medical Center Drive Rockville, MD 20850, USA

*To whom correspondence should be addressed. Tel: +1 301 795 7558; Fax: +1 301 838 0208; Email: rbuell{at}tigr.org

Received August 14, 2006. Revised October 26, 2006. Accepted October 26, 2006.

In The Institute for Genomic Research Rice Genome Annotation project (http://rice.tigr.org), we have continued to update the rice genome sequence with new data and improve the quality of the annotation. In our current release of annotation (Release 4.0; January 12, 2006), we have identified 42 653 non-transposable element-related genes encoding 49 472 gene models as a result of the detection of alternative splicing. We have refined our identification methods for transposable element-related genes resulting in 13 237 genes that are related to transposable elements. Through incorporation of multiple transcript and proteomic expression data sets, we have been able to annotate 24 799 genes (31 739 gene models), representing ~50% of the total gene models, as expressed in the rice genome. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 59 tracks. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads.


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