GoPipe: Streamlined Gene Ontology annotation for batch anonymous sequences with statistics
文献类型：期刊论文
| 作者 | Chen, ZZ; Xue, CH; Zhu, S; Zhou, FF; Ling, XFB; Liu, GP; Chen, LB |
| 刊名 | PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS
 |
| 出版日期 | 2005-02-01 |
| 卷号 | 32期号:2页码:187-190 |
| 关键词 | Gene Ontology functional genomics EST BLAST InterProScan GOA |
| 英文摘要 | Accelerated availability of new sequences, especially ESTs, calls for computational methods to link sequences with Gene Ontology (GO) terms in a batch mode. There is currently no program for such purpose except Goblet, an online tool which uses BLAST to interpret query sequence with proper GO terms, but has a restriction of upload sequence files less than 100 kilobytes in size. GoPipe is a standalone package that integrates BLAST and InterProScan results to obtain Gene Ontology annotation with built-in statistical options. GoPipe takes any number of BLAST and/or InterProScan output files simultaneously and launches jobs sequentially to perform parsing, data integration, redundancy removal, GO distributions calculation and graphic display. A very high annotation specificity of 99.1% was achieved for a test dataset when the program was run in the "intersection" mode, which intersects the BLAST and InterProScan results, outperforming the specificity (81.1%) obtained from the InterProScan only. Statistical tools are also provided to compare GO distributions between different inputs, so that GO distributions of different sets of batch sequences can be compared, and differentially represented GO terms can be easily displayed. High specificity, speed and flexibility make GoPipe an ideal tool for streamlined GO annotation for batch sequences. The package is freely available at http://gopipe.fishgenome.org/ or by contacting the authors. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 类目[WOS] | Biochemistry & Molecular Biology ; Biophysics |
| 研究领域[WOS] | Biochemistry & Molecular Biology ; Biophysics |
| 关键词[WOS] | DATABASE ; INTERPRO ; GO |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000227112400015 |
| 公开日期 | 2015-12-24 |
| 源URL | [http://ir.ia.ac.cn/handle/173211/9148]  |
| 专题 | 自动化研究所_09年以前成果 |
| 作者单位 | 1.Chinese Acad Sci, Inst Genet & Dev Biol, Beijing 100080, Peoples R China 2.Zhejiang Univ, Coll Life Sci, Hangzhou 310029, Peoples R China 3.Chinese Acad Sci, Inst Automat, Beijing 100080, Peoples R China 4.Univ Sci & Technol China, Natl High Performance Comp Ctr, Dept Comp Sci, Hefei 230027, Peoples R China 5.Tularik Inc, San Francisco, CA 94080 USA 6.Univ Glamorgan, Sch Elect, Pontypridd CF37 1DL, M Glam, Wales |
| 推荐引用方式 GB/T 7714 | Chen, ZZ,Xue, CH,Zhu, S,et al. GoPipe: Streamlined Gene Ontology annotation for batch anonymous sequences with statistics[J]. PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS,2005,32(2):187-190. |
| APA | Chen, ZZ.,Xue, CH.,Zhu, S.,Zhou, FF.,Ling, XFB.,...&Chen, LB.(2005).GoPipe: Streamlined Gene Ontology annotation for batch anonymous sequences with statistics.PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS,32(2),187-190. |
| MLA | Chen, ZZ,et al."GoPipe: Streamlined Gene Ontology annotation for batch anonymous sequences with statistics".PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS 32.2(2005):187-190. |
入库方式： OAI收割
来源：自动化研究所
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