期刊
DNA RESEARCH
卷 18, 期 6, 页码 435-449出版社
OXFORD UNIV PRESS
DOI: 10.1093/dnares/dsr030
关键词
protein-coding gene; microbial genome; re-annotation; horizontal gene transfer
资金
- National Natural Science Foundation of China [61073141, 30970561]
- Shandong Natural Science Foundation [ZR2010CQ041]
- Scientific Research Foundation of Graduate School of Southeast University [YBJJ1010]
The falsely annotated protein-coding genes have been deemed one of the major causes accounting for the annotating errors in public databases. Although many filtering approaches have been designed for the over-annotated protein-coding genes, some are questionable due to the resultant increase in false negative. Furthermore, there is no webserver or software specifically devised for the problem of over-annotation. In this study, we propose an integrative algorithm for detecting the over-annotated protein-coding genes in microorganisms. Overall, an average accuracy of 99.94% is achieved over 61 microbial genomes. The extremely high accuracy indicates that the presented algorithm is efficient to differentiate the protein-coding genes from the non-coding open reading frames. Abundant analyses show that the predicting results are reliable and the integrative algorithm is robust and convenient. Our analysis also indicates that the over-annotated protein-coding genes can cause the false positive of horizontal gene transfers detection. The webserver of the proposed algorithm can be freely accessible from www.cbi.seu.edu.cn/RPGM.
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