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

doi:10.1007/s11390-005-0446-x

	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
	2005
会议日期	JUN, 2004
会议地点	Tsinghua, PEOPLES R CHINA
关键词	DRAFT SEQUENCE DNA-SEQUENCES IDENTIFICATION CHROMOSOME-4 JAPONICA SEARCH MODELS BLAST
卷号	20
期号	4
DOI	10.1007/s11390-005-0446-x
页码	446-453
英文摘要	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.
会议录	JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
会议录出版者	SCIENCE PRESS
会议录出版地	BEIJING
语种	英语
URL标识	查看原文
ISSN号	1000-9000
WOS研究方向	Computer Science
内容类型	会议论文
源URL	[http://ir.itp.ac.cn/handle/311006/23700]
专题	SCI会议论文
作者单位	1.Suzhou Univ, Dept Math, Suzhou 215006, Peoples R China 2.Fudan Univ, T Life Res Ctr, Shanghai 200433, Peoples R China 3.BGI, Hangzhou Branch, Hangzhou 310008, Peoples R China 4.Acad Sinica, Inst Syst Sci, Beijing 100080, Peoples R China 5.Beijing Normal Univ, Dept Math, Beijing 100875, Peoples R China 6.Acad Sinica, Beijing Genom Inst, Beijing 101300, Peoples R China 7.Acad Sinica, Inst Theoret Phys, Beijing 100080, 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[C]. 见:. Tsinghua, PEOPLES R CHINA. JUN, 2004.