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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
Conference Name2nd Tsinghua International Bioinformatics Workshop
Source PublicationJOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
Volume20
Issue4
Pages446-453
Conference DateJUN, 2004
Conference PlaceTsinghua, PEOPLES R CHINA
Publication PlaceBEIJING
ISSN1000-9000
PublisherSCIENCE PRESS
AbstractWith 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.
KeywordDRAFT SEQUENCE DNA-SEQUENCES IDENTIFICATION CHROMOSOME-4 JAPONICA SEARCH MODELS BLAST
DOI10.1007/s11390-005-0446-x
URL查看原文
Indexed ByCPCI
Language英语
WOS Research AreaComputer Science
WOS SubjectComputer Science, Hardware & Architecture ; Computer Science, Software Engineering
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Cited Times:12[WOS]   [WOS Record]     [Related Records in WOS]
Document Type会议论文
Identifierhttp://ir.itp.ac.cn/handle/311006/23700
CollectionSCI会议论文
Affiliation1.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
Recommended Citation
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]. BEIJING:SCIENCE PRESS,2005:446-453.
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