Test data sets and evaluation of gene prediction programs on the rice genome

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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
	2005-07-01
发表期刊	JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
ISSN	1000-9000
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.
关键词	gene prediction rice genome test sets accuracy measures hidden Markov models dynamic programming
语种	英语
WOS研究方向	Computer Science
WOS类目	Computer Science, Hardware & Architecture ; Computer Science, Software Engineering
WOS记录号	WOS:000230712400004
出版者	SCIENCE PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/2115
专题	中国科学院数学与系统科学研究院
通讯作者	Hao, BL
作者单位	1.Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China 2.Acad Sinica, Beijing Genom Inst, Beijing 101300, Peoples R China 3.Beijing Normal Univ, Dept Math, Beijing 100875, Peoples R China 4.Acad Sinica, Inst Syst Sci, Beijing 100080, Peoples R China 5.BGI, Hangzhou Branch, Hangzhou 310008, Peoples R China 6.Suzhou Univ, Dept Math, Suzhou 215006, Peoples R China 7.Fudan Univ, T Life Res Ctr, Shanghai 200433, Peoples R China
推荐引用方式 GB/T 7714	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.(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.