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Nucleic Acids Research, 2004, Vol. 32, Database issue D377-D382
© 2004 Oxford University Press

BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics

Wenming Zhao1, Jing Wang2, Ximiao He1, Xiaobing Huang1, Yongzhi Jiao1, Mingtao Dai1, Shulin Wei1, Jian Fu1, Ye Chen1, Xiaoyu Ren1, Yong Zhang1,2, Peixiang Ni1, Jianguo Zhang1, Songgang Li1,2, Jian Wang1, Gane Ka-Shu Wong1,3, Hongyu Zhao4, Jun Yu1, Huanming Yang1 and Jun Wang*,1

1 Beijing Genomics Institute (BGI), Chinese Academy of Sciences (CAS), Beijing Airport Industrial Zone-B6, Beijing 101300, China, 2 College of Life Sciences, Peking University, Beijing 100871, China, 3 University of Washington Genome Center, Department of Medicine, Seattle, WA 98195, USA and 4 Yale University School of Medicine, Department of Epidemiology and Public Health, New Haven, CT 06520-8034, USA

*To whom correspondence should be addressed. Tel: +86 10 80481662; Fax: +86 10 80498676; Email: wangj{at}genomics.org.cn
Correspondence may also be addressed to Huanming Yang. Tel: +86 10 80494969; Fax: +86 10 80491181; Email: yanghm{at}genomics.org.cn
The authors wish it to be known that, in their opinion, the first four authors should be regarded as joint First Authors

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/).


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