The TIGR Rice Genome Annotation Resource: improvements and new features

TLDR

The TIGR Rice Genome Annotation project has updated the rice genome sequence, incorporated transcriptomic and proteomic data to annotate roughly 50 % of gene models, and made structural and functional annotations available through a browser, FTP, and a Data Extractor tool. Release 4.0 identified 42,653 non‑transposable element genes (49,472 models) via alternative splicing and refined TE gene detection to 13,237 TE‑related genes.

Abstract

In The Institute for Genomic Research Rice Genome Annotation project (Author Webpage), 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.