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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
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| 2005 | |
| Conference Name | 2nd Tsinghua International Bioinformatics Workshop |
| Source Publication | JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY |
| Volume | 20 |
| Issue | 4 |
| Pages | 446-453 |
| Conference Date | JUN, 2004 |
| Conference Place | Tsinghua, PEOPLES R CHINA |
| Publication Place | BEIJING |
| ISSN | 1000-9000 |
| Publisher | SCIENCE PRESS |
| Abstract | 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. |
| Keyword | DRAFT SEQUENCE DNA-SEQUENCES IDENTIFICATION CHROMOSOME-4 JAPONICA SEARCH MODELS BLAST |
| DOI | 10.1007/s11390-005-0446-x |
| URL | 查看原文 |
| Indexed By | CPCI |
| Language | 英语 |
| WOS Research Area | Computer Science |
| WOS Subject | Computer Science, Hardware & Architecture ; Computer Science, Software Engineering |
| Citation statistics | |
| Document Type | 会议论文 |
| Identifier | http://ir.itp.ac.cn/handle/311006/23700 |
| Collection | SCI会议论文 |
| Affiliation | 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 |
| 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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