title: BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics.
abstract: Rice is a major food staple for the world's population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing, information analysis and biological research of the rice and other crop genomes. In order to facilitate the application of the rice genomic information and to provide a foundation for functional and evolutionary studies of other important cereal crops, we implemented our Rice Information System (BGI-RIS), the most up-to-date integrated information resource as well as a workbench for comparative genomic analysis. In addition to comprehensive data from Oryza sativa L. ssp. indica sequenced by BGI, BGI-RIS also hosts carefully curated genome information from Oryza sativa L. ssp. japonica and EST sequences available from other cereal crops. In this resource, sequence contigs of indica (93-11) have been further assembled into Mbp-sized scaffolds and anchored onto the rice chromosomes referenced to physical/genetic markers, cDNAs and BAC-end sequences. We have annotated the rice genomes for gene content, repetitive elements, gene duplications (tandem and segmental) and single nucleotide polymorphisms between rice subspecies. Designed as a basic platform, BGI-RIS presents the sequenced genomes and related information in systematic and graphical ways for the convenience of in-depth comparative studies (http://rise.genomics.org.cn/).
authors.affiliation: Beijing Genomics Institute (BGI), Chinese Academy of Sciences (CAS), Beijing Airport Industrial Zone-B6, Beijing 101300, China.
authors.forename: Wenming
authors.initials: W
authors.lastname: Zhao
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Ximiao
authors.initials: X
authors.lastname: He
authors.forename: Xiaobing
authors.initials: X
authors.lastname: Huang
authors.forename: Yongzhi
authors.initials: Y
authors.lastname: Jiao
authors.forename: Mingtao
authors.initials: M
authors.lastname: Dai
authors.forename: Shulin
authors.initials: S
authors.lastname: Wei
authors.forename: Jian
authors.initials: J
authors.lastname: Fu
authors.forename: Ye
authors.initials: Y
authors.lastname: Chen
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Ren
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Peixiang
authors.initials: P
authors.lastname: Ni
authors.forename: Jianguo
authors.initials: J
authors.lastname: Zhang
authors.forename: Songgang
authors.initials: S
authors.lastname: Li
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.forename: Hongyu
authors.initials: H
authors.lastname: Zhao
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D002681:China; D019295:Computational Biology; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D018745:Genome, Plant; D023281:Genomics; D016247:Information Storage and Retrieval; D020407:Internet; D012275:Oryza / Q000235:genetics*; D012984:Software; D014584:User-Computer Interface