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

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

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.

Keywords: Agrobacterium tumefaciens strain C58 protein-coding gene genome re-annotation graphical representation

Received: 22 January 2015
Revised: 02 April 2015
Accepted manuscript online:

PACS:	82.39.Pj	(Nucleic acids, DNA and RNA bases?)
	87.14.gk	(DNA)

Fund: 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.

Corresponding Authors: Yu Jia-Feng
E-mail: jfyu1979@126.com

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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 2015 Chin. Phys. B 24 128202

[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

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

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