Computational prediction of over-annotated protein-coding genes in the genome of Agrobacterium tumefaciens strain C58

doi:10.1088/1674-1056/24/12/128202

中国物理B ›› 2015, Vol. 24 ›› Issue (12): 128202-128202.doi: 10.1088/1674-1056/24/12/128202

• SPECIAL TOPIC—8th IUPAP International Conference on Biological Physics • 上一篇下一篇

Computational prediction of over-annotated protein-coding genes in the genome of Agrobacterium tumefaciens strain C58

于家峰^{a b}, 隋天翔^{a d}, 王红梅^c, 王春玲^c, 荆莉^c, 王吉华^{a c}

a Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China;
b State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China;
c College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China;
d College of Life Science, Shandong Normal University, Jinan 250014, China

收稿日期:2015-01-22 修回日期:2015-04-02 出版日期:2015-12-05 发布日期:2015-12-05
通讯作者: Yu Jia-Feng E-mail:jfyu1979@126.com
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 61302186 and 61271378) and the Funding from the State Key Laboratory of Bioelectronics of Southeast University.

Computational prediction of over-annotated protein-coding genes in the genome of Agrobacterium tumefaciens strain C58

Yu Jia-Feng (于家峰)^{a b}, Sui Tian-Xiang (隋天翔)^{a d}, Wang Hong-Mei (王红梅)^c, Wang Chun-Ling (王春玲)^c, Jing Li (荆莉)^c, Wang Ji-Hua (王吉华)^{a c}

a Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China;
b State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China;
c College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China;
d College of Life Science, Shandong Normal University, Jinan 250014, China

Received:2015-01-22 Revised:2015-04-02 Online:2015-12-05 Published:2015-12-05
Contact: Yu Jia-Feng E-mail:jfyu1979@126.com
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 61302186 and 61271378) and the Funding from the State Key Laboratory of Bioelectronics of Southeast University.

摘要/Abstract

摘要： Agrobacterium tumefaciens strain C58 is a type of pathogen that can cause tumors in some dicotyledonous plants. Ever since the genome of A. tumefaciens strain C58 was sequenced, the quality of annotation of its protein-coding genes has been queried continually, because the annotation varies greatly among different databases. In this paper, the questionable hypothetical genes were re-predicted by integrating the TN curve and Z curve methods. As a result, 30 genes originally annotated as “hypothetical” were discriminated as being non-coding sequences. By testing the re-prediction program 10 times on data sets composed of the function-known genes, the mean accuracy of 99.99% and mean Matthews correlation coefficient value of 0.9999 were obtained. Further sequence analysis and COG analysis showed that the re-annotation results were very reliable. This work can provide an efficient tool and data resources for future studies of A. tumefaciens strain C58.

关键词: Agrobacterium tumefaciens strain C58, protein-coding gene, genome re-annotation, graphical representation

Abstract: Agrobacterium tumefaciens strain C58 is a type of pathogen that can cause tumors in some dicotyledonous plants. Ever since the genome of A. tumefaciens strain C58 was sequenced, the quality of annotation of its protein-coding genes has been queried continually, because the annotation varies greatly among different databases. In this paper, the questionable hypothetical genes were re-predicted by integrating the TN curve and Z curve methods. As a result, 30 genes originally annotated as “hypothetical” were discriminated as being non-coding sequences. By testing the re-prediction program 10 times on data sets composed of the function-known genes, the mean accuracy of 99.99% and mean Matthews correlation coefficient value of 0.9999 were obtained. Further sequence analysis and COG analysis showed that the re-annotation results were very reliable. This work can provide an efficient tool and data resources for future studies of A. tumefaciens strain C58.

Key words: Agrobacterium tumefaciens strain C58, protein-coding gene, genome re-annotation, graphical representation

中图分类号: (Nucleic acids, DNA and RNA bases?)

82.39.Pj

87.14.gk (DNA)

于家峰, 隋天翔, 王红梅, 王春玲, 荆莉, 王吉华. Computational prediction of over-annotated protein-coding genes in the genome of Agrobacterium tumefaciens strain C58[J]. 中国物理B, 2015, 24(12): 128202-128202.

Yu Jia-Feng (于家峰), Sui Tian-Xiang (隋天翔), Wang Hong-Mei (王红梅), Wang Chun-Ling (王春玲), Jing Li (荆莉), Wang Ji-Hua (王吉华). Computational prediction of over-annotated protein-coding genes in the genome of Agrobacterium tumefaciens strain C58[J]. Chin. Phys. B, 2015, 24(12): 128202-128202.

参考文献 23

[1]	Kyrpides N C 2009 Nat. Biotechnol. 27 627
[2]	Petty N K 2010 Nat. Rev. Microbiol. 8 762
[3]	Yu J F, Guo Z Z, Sun X and Wang J H 2014 Curr. Bioinformatics 9 147
[4]	Yu J F, Xiao K, Jiang D K, Guo J, Wang J H and Sun X 2011 DNA Res. 18 435
[5]	Zhang C T and Zhang R 1991 Nucleic Acids Res. 19 6313
[6]	Yu J F, Sun X and Wang J H 2009 J. Theor. Biol. 261 459
[7]	Wood D, Setubal J, Kaul R, et al. 2001 Science 294 2317
[8]	Pruitt K D, Tatusova T and Maglott D R 2007 Nucleic Acids Res. 35 61
[9]	Gao F and Zhang C T 2004 Bioinformatics 20 673
[10]	Yu J F and Sun X 2010 J. Comput. Chem. 31 2126
[11]	Yu J F, Guo J, Liu Q B, Hou Y, Xiao K, Chen Q L, Wang J H and Sun X 2015 Genes Genom. 37 347
[12]	Zhang C T and Wang J 2000 Nucleic Acids Res. 28 2804
[13]	Burset M and Guigo R 1996 Genomics 34 353
[14]	Trifonov E N 1987 J. Mol. Biol. 194 643
[15]	Tatusov R L, Galperin M Y, Natale D A and Koonin E V 2000 Nucleic Acids Res. 28 33
[16]	Wang Q, Lei Y, Xu X, Wang G J and Chen L L 2013 PLoS One 7 e43176
[17]	Liolios K, Chen I A, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz V M and Kyrpides N C 2010 Nucleic Acids Res. 38 D346
[18]	Reed J L, Famili I, Thiele I and Palsson B O 2006 Nat. Rev. Genet. 7 130
[19]	Reeves G A, Talavera D and Thornton J M 2009 J. R. Soc. Interface 6 129
[20]	Skovgaard M, Jensen L J, Brunak S, Ussery D and Krogh A 2001 Trends Genet. 17 425
[21]	Salzberg S L 2007 Genome Biol. 8 102
[22]	Bakke P, Carney N, DeLoache W, Gearing M, Ingvorsen K, Lotz M, McNair J, Penumetcha P, Simpson S, Voss L, Win M, Heyer L and Campbell A 2009 PLoS One 4 e6291
[23]	Yu J F, Jiang D K, Jin Y, Wang J H and Sun X 2012 MATCH. Commun. Math. Comput. Chem. 67 845

Computational prediction of over-annotated protein-coding genes in the genome of Agrobacterium tumefaciens strain C58

Computational prediction of over-annotated protein-coding genes in the genome of Agrobacterium tumefaciens strain C58

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