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Genomics Inform > Volume 5(4); 2007 > Article
RGISS: Rice (Oryza sativa L. ssp. japonica) Genome Information Service System.
Daesang Lee, Hwajung Seo, Jang Ho Hahn, Eun Bae Kong, Kiejung Park
1Department of Bioinformatics, Korea Bio Polytechnic, Chungnam 320-905, Korea.
2Department of Computer Engineering, Chungnam National University, Daejeon 305-764, Korea.
3National Institute of Agricultural Biotechnology, RDA, Suwon 441-707, Korea.
4Information Technology Institute, SmallSoft Co. Ltd., Daejeon 305-342, Korea. kjpark@smallsoft.co.kr
Abstract
We have constructed the Rice Genome Information Service System (RGISS), which is an information service system of the Oryza sativa L. ssp. japonica (rice) genome, using the released version of rice Build 3.0 pseudomolecules based on the Ensembl architecture. The nonredundant library, composed of 3,360 clones of BACs, PACs, and fosmids, was used to construct supercontigs. RGISS contains 50,717 annotated genes from GenBank, 56,161 predicted genes from FgeneSH, and information on 9,587 markers, which includes STS, SSR, and EST-based RFLP. The 20,180 ESTs sequenced by the Korea National Institute of Agricultural Biotechnology (NIAB) were aligned and mapped into 168,792 exons. By gene ontology analysis, the classified protein numbers in the rice genome were 6158, 4531, and 12,364 proteins, which were mapped to molecular function, cellular component, and biological process, respectively.
Keywords: rice; annotation; Ensembl; EST; marker
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