title: 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.
authors.affiliation: The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
authors.forename: Shu
authors.initials: S
authors.lastname: Ouyang
authors.forename: Wei
authors.initials: W
authors.lastname: Zhu
authors.forename: John
authors.initials: J
authors.lastname: Hamilton
authors.forename: Haining
authors.initials: H
authors.lastname: Lin
authors.forename: Matthew
authors.initials: M
authors.lastname: Campbell
authors.forename: Kevin
authors.initials: K
authors.lastname: Childs
authors.forename: Françoise
authors.initials: F
authors.lastname: Thibaud-Nissen
authors.forename: Renae L
authors.initials: RL
authors.lastname: Malek
authors.forename: Yuandan
authors.initials: Y
authors.lastname: Lee
authors.forename: Li
authors.initials: L
authors.lastname: Zheng
authors.forename: Joshua
authors.initials: J
authors.lastname: Orvis
authors.forename: Brian
authors.initials: B
authors.lastname: Haas
authors.forename: Jennifer
authors.initials: J
authors.lastname: Wortman
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
mesh_terms: D004251:DNA Transposable Elements; D018076:DNA, Complementary / Q000737:chemistry; D030541:Databases, Genetic; D020224:Expressed Sequence Tags / Q000737:chemistry; D015870:Gene Expression; D018745:Genome, Plant; D020407:Internet; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D040901:Proteomics; D014584:User-Computer Interface
chemical_list: D004251:DNA Transposable Elements; D018076:DNA, Complementary