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This article is part of the supplement: The International Conference on Intelligent Biology and Medicine (ICIBM) – Genomics

Open Access Research

Detecting the borders between coding and non-coding DNA regions in prokaryotes based on recursive segmentation and nucleotide doublets statistics

Suping Deng12, Yixiang Shi3, Liyun Yuan34, Yixue Li23 and Guohui Ding2*

Author affiliations

1 School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, P.R. China

2 Key lab of systems biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, P.R.China

3 Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai, 200235, P. R. China

4 Shanghai Jiaotong University, Shanghai, 200240, P. R. China

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Citation and License

BMC Genomics 2012, 13(Suppl 8):S19  doi:10.1186/1471-2164-13-S8-S19

Published: 17 December 2012

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.