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A hybrid strategy for comprehensive annotation of the protein coding genes in prokaryotic genome

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Abstract

Protein coding gene annotation errors in prokaryotic genomes are accumulating continually in bioinformatics databases, while the update rate of genome annotation can not keep up with the explosive increasing genome sequences in most cases. Hence it is critical to manually rectify the genome annotation errors. In this paper, a hybrid strategy by combing the gene ab initio predicting programs and the over annotated gene re-annotation programs is proposed for re-annotation of the protein coding genes in prokaryotic genomes. Based on this strategy, the protein coding genes in Geobacter sulfurreducens PCA is comprehensively re-annotated. As a consequence, 16 hypothetical genes are annotated as non-coding sequences and 104 missing genes are retrieved as protein coding genes. Subsequent function analysis and sequences analysis show that the predicting results are much reliable and robust. Further application to other genomes show that this work can provide alternative tools for later post-process of prokaryotic genome annotations.

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Acknowledgments

This work was supported by National Natural Science Foundation of China (Projects No. 61302186 and No. 61271378), Shandong Natural Science Foundation (Project No. ZR2010CQ041) and the funding from the State Key Laboratory of Bioelectronics of Southeast University.

Conflict of interest

The authors declare that there is no conflict of interest.

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Authors and Affiliations

  1. Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, People’s Republic of China

    Jia-Feng Yu, Qing-Bin Liu, Qing-Li Chen & Ji-Hua Wang

  2. State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096, People’s Republic of China

    Jia-Feng Yu, Yue Hou, Ke Xiao & Xiao Sun

  3. College of Physics and Electronic Information, Dezhou University, Dezhou, 253023, People’s Republic of China

    Jia-Feng Yu & Ji-Hua Wang

  4. School of Computer Engineering, Nanyang Technological University, Singapore, 639798, Singapore

    Jing Guo

  5. College of Life Science, Shandong Normal University, Jinan, 250014, People’s Republic of China

    Qing-Bin Liu & Qing-Li Chen

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  1. Jia-Feng Yu
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  2. Jing Guo
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  3. Qing-Bin Liu
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  4. Yue Hou
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  5. Ke Xiao
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  6. Qing-Li Chen
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  7. Ji-Hua Wang
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  8. Xiao Sun
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Correspondence to Jia-Feng Yu or Xiao Sun.

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Yu, JF., Guo, J., Liu, QB. et al. A hybrid strategy for comprehensive annotation of the protein coding genes in prokaryotic genome. Genes Genom 37, 347–355 (2015). https://doi.org/10.1007/s13258-014-0263-0

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  • DOI: https://doi.org/10.1007/s13258-014-0263-0

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