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

Nucleic Acids Research

Volumn 32, Issue DATABASE ISS., 2004, Pages

  Zhao, Wenming ^a   Wang, Jing ^b   He, Ximiao ^a   Huang, Xiaobing ^a   Jiao, Yongzhi ^a   Dai, Mingtao ^a   Wei, Shulin ^a   Fu, Jian ^a   Chen, Ye ^a   Ren, Xiaoyu ^a   Zhang, Yong ^a,b   Ni, Peixiang ^a   Zhang, Jianguo ^a   Li, Songgang ^a,b   Wang, Jian ^a   Wong, Gane Ka Shu ^a,c   Zhao, Hongyu ^d   Yu, Jun ^a   Yang, Huanming ^a   Wang, Jun ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b PEKING UNIVERSITY   (China)

^c UNIVERSITY OF WASHINGTON   (United States)

^d YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; CONTIG; REPETITIVE DNA;

ARTICLE; BEIJING GENOMICS INSTITUTE-RICE INFORMATION SYSTEM; BIOLOGICAL MODEL; CEREAL; COMPARATIVE STUDY; CONTROLLED STUDY; CROP; EXPRESSED SEQUENCE TAG; FOOD; GENE DUPLICATION; GENE SEQUENCE; GENETIC DATABASE; GENETIC MARKER; GENETIC RESOURCE; GENOME ANALYSIS; INFORMATION PROCESSING; INFORMATION SYSTEM; MOLECULAR EVOLUTION; NONHUMAN; PLANT CHROMOSOME; PLANT GENETICS; POPULATION; PRIORITY JOURNAL; RICE; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE; SYSTEM ANALYSIS; TANDEM REPEAT;

CHINA; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENOME, PLANT; GENOMICS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; ORYZA SATIVA; SOFTWARE; USER-COMPUTER INTERFACE;

EMBRYOPHYTA; JAPONICA; ORYZA SATIVA;

EID: 9144231248     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (20)

1. Yu,J., Hu,S.N., Wang,J., Gane,K.W., Li,S.G., Liu,B., Deng,Y.J., Li,D., Zhou,Y., Zhang X. Q. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296, 79-92.
2. Goff,S.A., Ricke,D., Lan, T-H., Presting,G., Wang,R., Dunn,M., Glazebrook,J., Sessions,A., Oeller,P., Varma,H. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92-100.
3. Chen,M., SanMiguel,P., De Oliveira,A.C., Woo,S.-S., Zhang,H., Wing,R.A. and Bennetzen,J.L. (1997) Microcolinearity in sh2-homologous regions of the maize, rice and sorghum genomes. Proc. Natl Acad. Sci. USA, 94, 3431-3435.
4. Bevan,M. and Murphy,G. (1999) The small, the large and the wild - the value of comparison in plant genomics. Plant Genomics, 15, 211-215.
5. McCouch,S. (1998) Toward a plant genomics initiative: thought on the value of cross-species and cross-genera comparisons in the grasses. Proc. Natl Acad. Sci. USA, 95, 1983-1985.
6. Kikuchi,S., Satoh,K., Nagata,T., Kawagashira,N., Doi,K., Kishimoto,N., Yazaki,J., Ishikawa,M., Yamada,H., Ooka,H. et al. (2003) Collection, mapping and annotation of over 28,000 cDNA clones from japonica rice. Science, 301, 376-379.
7. Burge,Ch. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
8. Burset,M. and Guigo,R. (1996) Evaluation of gene structure prediction programs. Genomics, 34, 353-367.
9. Fickett,J.W. (1996) Finding genes by computer: the state of the art. Trends Genet., 12, 316-320.
10. Bellman,R. (1957) Dynamic Programming. Princeton University Press, Princeton, NJ.
11. Bellman,R. and Dreyfus,S.E. (1962) Applied Dynamic Programming. Princeton University Press, Princeton, NJ.
12. Krogh,A., Mian,I.S. and Haussler,D. (1994) A hidden Markov model that finds genes in E. coli DNA. Nucleic Acids Res., 22, 4768-4778.
13. Krogh,A., Brown,M., Mian,I.S., Sjolander,K. and Haussler,D. (1994) Hidden Markov Models in computational biology applications to protein modeling. J. Mol. Biol., 235, 1501-1531.
14. Rabiner,L.R. and Juang,B.H. (1986) An introduction to Hidden Markov Models. IEEE ASSP Mag., 3, 4-16.
15. Ewing,B. and Green,P. (1998) Basecalling of automated sequencer traces using Phred. II. Error probabilities. Genome Res., 8, 186-194.
16. Ware,D., Jaiswal,P., Ni,J., Pan,X., Chang,K., Clark,K., Teytelman,L., Schmidt,S., Zhao,W., Cartinhour,S. et al. (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Res., 30, 103-105.
17. Hubbard,T. Barker,D., Birney,E., Cameron,G., Chen,Y., Clark,L., Cox,T., Cuff,J., Curwen,V., Down,T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41.
18. Tatusov,R.L., Natale,D.A., Garkavtsev,I.V., Tatusova,T.A., Shankavaram,U.T., Rao,B.S., Kiryutin,B., Galperin,M.Y., Fedorova,N.D. and Koonin,E.V. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res., 29, 22-28.
19. Kellogg,E.A. (1999) Relationships of cereal crops and other grasses. Proc. Natl Acad. Sci. USA, 95, 2005-2010.
20. Jurka,J. (1998) Repeats in genomic DNA: mining and meaning. Curr. Opin. Struct. Biol., 8, 333-337.