Test data sets and evaluation of gene prediction programs on the rice genome
文献类型：期刊论文
| 作者 | Li, H; Liu, JS; Xu, Z; Jin, J; Fang, L; Gao, L; Li, YD; Xing, ZX; Gao, SG; Liu, T |
| 刊名 | JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
 |
| 出版日期 | 2005-07-01 |
| 卷号 | 20期号:4页码:446-453 |
| 关键词 | gene prediction rice genome test sets accuracy measures hidden Markov models dynamic programming |
| ISSN号 | 1000-9000 |
| 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. |
| WOS研究方向 | Computer Science |
| 语种 | 英语 |
| WOS记录号 | WOS:000230712400004 |
| 出版者 | SCIENCE PRESS |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/2114]  |
| 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. |
入库方式： OAI收割
来源：数学与系统科学研究院
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