The TIGR Rice Genome Annotation Resource: improvements and new features

Abstract

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 approximately 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.

Figure 1

Display of EST read pairs in the TIGR Rice Genome Browser. Shown is a rice locus (LOC_Os02g42040) which lacks full-length cDNA support yet has empirical support for the 5′ and 3′ termini through multiple EST read pairs. The direction of the EST read pairs is indicated by an arrow and the 5′-termini is colored in green while the 3′-termini in red.

Figure 2

Segmental duplication within rice. Segmentally duplicated blocks among the 12 rice chromosomes are hyperlinked to gene lists, thereby allowing the users to navigate between a genome level view of the segmental duplication and annotation at the gene level annotation. The figure displays the segmental duplication within the rice genome generated using 100 kb as the maximum distance allowed between two collinear gene pairs.