title: An integrative method for identifying the over-annotated protein-coding genes in microbial genomes.
abstract: 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.
authors: State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China. jfyu1979@126.com
authors: Jia-Feng
authors: JF
authors: Yu
authors: Ke
authors: K
authors: Xiao
authors: Dong-Ke
authors: DK
authors: Jiang
authors: Jing
authors: J
authors: Guo
authors: Ji-Hua
authors: JH
authors: Wang
authors: Xiao
authors: X
authors: Sun
mesh_terms: D000465:Algorithms; D019843:Archaeal Proteins / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D001482:Base Composition; D019295:Computational Biology / Q000379:methods; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D020407:Internet; D058977:Molecular Sequence Annotation / Q000379:methods*; D016366:Open Reading Frames; D012984:Software
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins