BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics.
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/).
Zhao
Wenming
W
Beijing Genomics Institute (BGI), Chinese Academy of Sciences (CAS), Beijing Airport Industrial Zone-B6, Beijing 101300, China.
Wang
Jing
J
He
Ximiao
X
Huang
Xiaobing
X
Jiao
Yongzhi
Y
Dai
Mingtao
M
Wei
Shulin
S
Fu
Jian
J
Chen
Ye
Y
Ren
Xiaoyu
X
Zhang
Yong
Y
Ni
Peixiang
P
Zhang
Jianguo
J
Li
Songgang
S
Wang
Jian
J
Wong
Gane Ka-Shu
GK
Zhao
Hongyu
H
Yu
Jun
J
Yang
Huanming
H
Wang
Jun
J
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