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Test data sets and evaluation of gene prediction programs on the rice genome
Li, H; Liu, JS; Xu, Z; Jin, J; Fang, L; Gao, L; Li, YD; Xing, ZX; Gao, SG; Liu, T; Li, HH; Li, Y; Fang, LJ; Xie, HM; Zheng, WM; Hao, BL; Hao, BL , Acad Sinica, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China.
2005
发表期刊JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
ISSN1000-9000
卷号20期号:4页码:446-453
摘要With several rice genome projects approaching completion gene prediction/finding by computer algorithms has become an urgent task. Two test sets were constructed by mapping the newly published 28,469 full-length KOME rice cDNA to the RGP BAC clone sequences of Oryza sativa ssp. japonica: a single-gene set of 550 sequences and a multi-gene set of 62 sequences with 271 genes. These data sets were used to evaluate five ab initio gene prediction programs: RiceHMM, GlimmerR, GeneMark, FGENSH and BGF. The predictions were compared on nucleotide, exon and whole gene structure levels using commonly accepted measures and several new measures. The test results show a progress in performance in chronological order. At the same time complementarity of the programs hints on the possibility of further improvement and on the feasibility of reaching better performance by combining several gene-finders.
部门归属Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China; Acad Sinica, Beijing Genom Inst, Beijing 101300, Peoples R China; Beijing Normal Univ, Dept Math, Beijing 100875, Peoples R China; Acad Sinica, Inst Syst Sci, Beijing 100080, Peoples R China; BGI, Hangzhou Branch, Hangzhou 310008, Peoples R China; Suzhou Univ, Dept Math, Suzhou 215006, Peoples R China; Fudan Univ, T Life Res Ctr, Shanghai 200433, Peoples R China
关键词Draft Sequence Dna-sequences Identification Chromosome-4 Japonica Search Models Blast
学科领域Physics
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收录类别SCI
WOS记录号WOS:000230712400004
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被引频次:8[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/13788
专题1978-2010年知识产出
通讯作者Hao, BL , Acad Sinica, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China.
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Li, H,Liu, JS,Xu, Z,et al. Test data sets and evaluation of gene prediction programs on the rice genome[J]. JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY,2005,20(4):446-453.
APA Li, H.,Liu, JS.,Xu, Z.,Jin, J.,Fang, L.,...&Hao, BL , Acad Sinica, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China..(2005).Test data sets and evaluation of gene prediction programs on the rice genome.JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY,20(4),446-453.
MLA Li, H,et al."Test data sets and evaluation of gene prediction programs on the rice genome".JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY 20.4(2005):446-453.
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