TIGR Rice Genome Annotation

Annotation and Informatics


		Rice Distributed Annotation System (DAS) All annotated rice BACs can now be viewed through our DAS viewer. Click here to read how the use the TIGR CGI based DAS viewer (In development). Whole Automated Rice Genome Annotation Database This database contains all rice BAC/PAC sequences in GenBank. These sequences were processed through an automated annotation pipeline. Annotated sequences can be searched on a BLAST server, searched by gene name, and are displayed based on their map position. TIGR Curated Rice Annotation Database This database contains every sequence derived from the TIGR rice genome sequencing project. Annotated sequences will be displayed based on their map position, can be searched on a blast server, and can be searched by gene name. TIGR Plant Ortholog Database As part of our Rice Genome Program, we are identifying putative orthologs and paralogs in our rice sequences. Click here to see the first release of the TIGR Plant Ortholog Database. Global Alignment of Plant Transcripts with Rice Genomic DNA We also perform global alignments of seven plant gene indices with our rice genome sequences. The resulting graphic display allows for identification of related transcripts from all plant species at the whole BAC level. We will be updating this web site in the future to include all rice genome seuqences, not just TIGR generated sequences. Click here for the current version of the Global Alignment of Plant Transcripts with Rice Genomic DNA. Rice Repeat Database The rice genome like those of other higher eukaryotes consists of repetitive DNA sequence intermixed with coding sequence. It is estimated that 50% of the rice genome is comprised of repetitive sequence. We have created this database to assist in the compilation and identification of repeats and mobile elements in the rice genome. Rice Gene Index (OsGI) All publicly available Rice ESTs as well as transcripts from GenBank have been assembled into contigs and built into the Oryza sativa Gene Index (OsGI).

For Rice Comments/Questions send mail to the TIGR rice team.

Photographs courtesy of Robin Buell (TIGR), Jiming Jiang (University of Wisconsin), and the USDA Agricultural Research Service