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GoPipe: Streamlined Gene Ontology annotation for batch anonymous sequences with statistics
Chen, ZZ; Xue, CH; Zhu, S; Zhou, FF; Ling, XFB; Liu, GP; Chen, LB
Source PublicationPROGRESS IN BIOCHEMISTRY AND BIOPHYSICS
2005-02-01
Volume32Issue:2Pages:187-190
SubtypeArticle
AbstractAccelerated 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.
KeywordGene Ontology Functional Genomics Est Blast Interproscan Goa
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
WOS KeywordDATABASE ; INTERPRO ; GO
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Biophysics
WOS SubjectBiochemistry & Molecular Biology ; Biophysics
WOS IDWOS:000227112400015
Citation statistics
Cited Times:66[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ia.ac.cn/handle/173211/9148
Collection09年以前成果
Affiliation1.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
Recommended Citation
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.
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