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

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• 作者：Jia-Feng Yu (1) (2) (3)
  Jing Guo (4)
  Qing-Bin Liu (1) (5)
  Yue Hou (2)
  Ke Xiao (2)
  Qing-Li Chen (1) (5)
  Ji-Hua Wang (1) (3)
  Xiao Sun (2)
  
  1. Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics ; Institute of Biophysics ; Dezhou University ; Dezhou ; 253023 ; People鈥檚 Republic of China
  2. State Key Laboratory of Bioelectronics ; Southeast University ; Nanjing ; 210096 ; People鈥檚 Republic of China
  3. College of Physics and Electronic Information ; Dezhou University ; Dezhou ; 253023 ; People鈥檚 Republic of China
  4. School of Computer Engineering ; Nanyang Technological University ; Singapore ; 639798 ; Singapore
  5. College of Life Science ; Shandong Normal University ; Jinan ; 250014 ; People鈥檚 Republic of China
  
• 关键词：Protein coding genes ; Re ; annotation ; Prokaryotic genome
• 刊名：Genes & Genomics
• 出版年：2015
• 出版时间：April 2015
• 年：2015
• 卷：37
• 期：4
• 页码：347-355
• 全文大小：516 KB
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• 刊物主题：Microbial Genetics and Genomics; Plant Genetics & Genomics; Animal Genetics and Genomics; Human Genetics;
• 出版者：Springer Netherlands
• ISSN：2092-9293

文摘

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.