title: Detecting the borders between coding and non-coding DNA regions in prokaryotes based on recursive segmentation and nucleotide doublets statistics.
abstract: BACKGROUND
  Detecting the borders between coding and non-coding regions is an essential step in the genome annotation. And information entropy measures are useful for describing the signals in genome sequence. However, the accuracies of previous methods of finding borders based on entropy segmentation method still need to be improved.
  
  
  METHODS
  In this study, we first applied a new recursive entropic segmentation method on DNA sequences to get preliminary significant cuts. A 22-symbol alphabet is used to capture the differential composition of nucleotide doublets and stop codon patterns along three phases in both DNA strands. This process requires no prior training datasets.
  
  
  RESULTS
  Comparing with the previous segmentation methods, the experimental results on three bacteria genomes, Rickettsia prowazekii, Borrelia burgdorferi and E.coli, show that our approach improves the accuracy for finding the borders between coding and non-coding regions in DNA sequences.
  
  
  CONCLUSIONS
  This paper presents a new segmentation method in prokaryotes based on Jensen-Rényi divergence with a 22-symbol alphabet. For three bacteria genomes, comparing to A12_JR method, our method raised the accuracy of finding the borders between protein coding and non-coding regions in DNA sequences.
authors.affiliation: School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, PR China.
authors.forename: Suping
authors.initials: S
authors.lastname: Deng
authors.forename: Yixiang
authors.initials: Y
authors.lastname: Shi
authors.forename: Liyun
authors.initials: L
authors.lastname: Yuan
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
authors.forename: Guohui
authors.initials: G
authors.lastname: Ding
mesh_terms: D000465:Algorithms; D025065:Borrelia burgdorferi / Q000235:genetics*; D018388:Codon, Terminator; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics*; D009711:Nucleotides / Q000737:chemistry; D016366:Open Reading Frames; D012283:Rickettsia prowazekii / Q000235:genetics*
chemical_list: D018388:Codon, Terminator; D004269:DNA, Bacterial; D009711:Nucleotides