January 24, 2007

• The Rice Genome Annotation Project database, website and genome browser have been updated.
• The TIGR Rice Genome Browser has been updated and contains 62 tracks of annotation. These tracks have been updated to contain the latest evidence and datasets.
• Gene model structure has been improved for 33,882 gene models (28,706 genes) with ~ 1.2 million of EST and/or full length cDNA evidence using the TIGR PASA program. A portion of models has been manually curated using the expression evidence and comparative genomics studies.
• The rice gene expression Anatomy Viewer/Digital Northern and Tissue Specific Expression page have been updated.
• The rice community annotation has been carried out, and the results have been integrated into the TIGR rice annotation.
• Locus names have been assigned to chloroplast and mitochondrial genes.
• A new protein function category, conserved hypothetical protein, has been introduced for proteins only matching to proteins without known function in other organisms.
• The maize genetic maps used to generate the rice/maize synteny information have been updated. We now provide alignments of the cIBM 2005 and the IBM2 2005 Neighbor maps to the rice pseudomolecules.
• Gene name assignment has been changed slightly. Hypothetical proteins that align with hypothetical or an uncharacterized proteins are now called conserved hypothetical proteins. See the Automatic Annotation description page for more information.
• A track of small RNAs has been added to the TIGR Rice Genome Browser. Small RNAs from the Cereal Small RNAs Database have been mapped to the pseudomolecules.

November 2, 2006

• The Rice Genome Browser has been updated.
• The results from InterProScan searches have been added as a new track in the browser.
• Oryza protein sequences from SwissProt were aligned to the rice pseudomolecules, and these data have been added as an additional track in the browser.
• The latest set of available Flanking Sequence Tags (FST) have been incorporated into the FST track in the browser.

October 17, 2006

• New Community Annotations have been added. Annotation from 23 gene families with a total of 454 genes has been provided by rice researchers. The newest contributions are:
• Annotation for twenty eight glutaredoxin genes has been added.
• Annotation for thirteen indole-3-acetic-acid synthetase genes has been added.

August 5, 2006

• The Rice Genome Browser has been updated.
• Tracks representing alignments of sequences from the TIGR Gene Indices have been removed.
• Tracks representing alignments with the TIGR Plant Transcript Assemblies have been added.
• A track of Interim TIGR Structural Gene Models as determined by PASA2 using the latest FL-cDNA and EST evidence has been added. These models will serve as the basis of the models in the version 5 release, but this data set has not yet been finalized.
• A new track of EST Read Pairs has been added. These data are derived from the ~750,000 read pairs that were generated by KOME. Those EST read pairs that aligned to the rice pseudomolecules in the proper orientation and in proximity to each other are displayed.
• A new expression track of Rice MPSS tags has been added.
• The tracks for Agilent, Affymetrix, Yale and NSF expression oligos have all been updated.
• The Protein Evidence track that shows the alignments of TIGR niaa proteins to the rice pseudomolecules has been updated with more stringent alignments.
• The track showing the alignment of Pack MULEs identified by Juretic et al. has been renamed "Pack MULEs (McGill)".
• The Flanking Sequence Tags track has been updated.

June 16, 2006

• A link to the 4th International Rice Functional Genomic Symposium has been added to the links page. This conference will be held in Montpellier, France from October 9th to October 11th.

May 17, 2006

• A track showing the alignment of Kasalath and OMap rice BAC-ends has been added to the Rice Genome Browser.

April 26, 2006

• Four new tracks have been added to the Rice Genome Browser:
• Alignments of Zea mays genomic sequences.
• Alignments of Sorghum bicolor genomic sequences
• Alignments of Arabidopsis thaliana genomic sequences
• NSF 45k Rice Oligo Microarray probes


• One track has been updated on the Rice Genome Browser:
• Flanking Sequence Tags

March 13, 2006

• The Rice Genome Browser has been updated to use version 1.64 of Genome Browser. The new version of Genome Browser allows users to collapse sections of the browser page in order to customize the page display.

February 17, 2006

• TIGR will be hosting its annual 5-day Annotation Workshop from June 26-30th. This workshop provides a comprehensive training in all aspects of the annotation of the rice genome. While this workshop focuses on rice, the fundamentals are broadly applicable to higher plant genomes. This workshop is geared towards biologically oriented graduate students and post-doctoral researchers who are interested in bioinformatics. Go to the Training Opportunities page to obtain more information and feel free to e-mail Matthew Campbell (campbell@tigr.org) with any questions.

January 12, 2006

• The Rice Genome Annotation Project (funded by the National Science Foundation) has released Release 4 of the rice genome annotation. A full description of the pseudomolecules is available here. In addition, we updated all of our other analyses such as Flanking Sequence Tag searches, alignment with the Gene Indices, alignment with maize/wheat genetic markers, domain and motifs, and our rice genome statistics.

• Our Rice Genome Browser was updated and now contains 45 tracks of annotation. These tracks have been updated to include the latest evidence and datasets.

• Gene model structure has been improved for 28,763 models with EST and/or full length cDNA evidence using the TIGR PASA program.

• Additional expression evidence (MPSS, SAGE, and proteomics data) was used to functionally annotate the gene models.

• The Expression Evidence page for expressed genes has been created.

• Regions of segmental duplication have been identified.

• Syntenic Mapping with Sorghum pages have been added

• Updated pseudomolecule based Pfam and Interpro Domain Searches.

• Updated pseudomolecule based motif predictions including Predotar predictions

• FST Insertions into the Release 4 models