IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v409y2014icp87-96.html
   My bibliography  Save this article

A novel representation of DNA sequence based on CMI coding

Author

Listed:
  • Hou, Wenbing
  • Pan, Qiuhui
  • He, Mingfeng

Abstract

Graphical representation of DNA sequences provides a simple and intuitive way of analyzing and sorting various gene sequences. It is attractive to researchers to propose much more appropriate methods. In this study, a new graphical representation is presented. The method adopts the CMI coding to represent four nucleotides-A, G, C and T. Our approach considers not only the sequences’ structure but also the chemical structure for DNA sequence. We take several sets of data to test our method. The results of our experiment demonstrate that our representation is effective.

Suggested Citation

  • Hou, Wenbing & Pan, Qiuhui & He, Mingfeng, 2014. "A novel representation of DNA sequence based on CMI coding," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 409(C), pages 87-96.
    • Handle: RePEc:eee:phsmap:v:409:y:2014:i:c:p:87-96
    DOI: 10.1016/j.physa.2014.04.030
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437114003410
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000
    File URL: https://libkey.io/10.1016/j.physa.2014.04.030?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. He, Ping-an & Wei, Jinzhou & Yao, Yuhua & Tie, Zhixin, 2012. "A novel graphical representation of proteins and its application," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(1), pages 93-99.
    2. Liao, Bo & Xiang, Qilin & Cai, Lijun & Cao, Zhi, 2013. "A new graphical coding of DNA sequence and its similarity calculation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 392(19), pages 4663-4667.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Jin, Xin & Nie, Rencan & Zhou, Dongming & Yao, Shaowen & Chen, Yanyan & Yu, Jiefu & Wang, Quan, 2016. "A novel DNA sequence similarity calculation based on simplified pulse-coupled neural network and Huffman coding," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 461(C), pages 325-338.
    2. Li, Yushuang & Liu, Qian & Zheng, Xiaoqi, 2016. "DUC-Curve, a highly compact 2D graphical representation of DNA sequences and its application in sequence alignment," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 456(C), pages 256-270.
    3. Qian, Kun & Luan, Yihui, 2018. "Phylogenetic analysis of DNA sequences based on fractional Fourier transform," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 509(C), pages 795-808.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Jin, Xin & Nie, Rencan & Zhou, Dongming & Yao, Shaowen & Chen, Yanyan & Yu, Jiefu & Wang, Quan, 2016. "A novel DNA sequence similarity calculation based on simplified pulse-coupled neural network and Huffman coding," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 461(C), pages 325-338.
    2. Qian, Kun & Luan, Yihui, 2017. "Weighted measures based on maximizing deviation for alignment-free sequence comparison," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 481(C), pages 235-242.
    3. Qian, Kun & Luan, Yihui, 2018. "Phylogenetic analysis of DNA sequences based on fractional Fourier transform," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 509(C), pages 795-808.
    4. Liao, Bo & Xiang, Qilin & Cai, Lijun & Cao, Zhi, 2013. "A new graphical coding of DNA sequence and its similarity calculation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 392(19), pages 4663-4667.
    5. Mahmoodi-Reihani, Mehri & Abbasitabar, Fatemeh & Zare-Shahabadi, Vahid, 2018. "A novel graphical representation and similarity analysis of protein sequences based on physicochemical properties," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 510(C), pages 477-485.
    6. Ma, Tingting & Liu, Yuxin & Dai, Qi & Yao, Yuhua & He, Ping-an, 2014. "A graphical representation of protein based on a novel iterated function system," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 403(C), pages 21-28.
    7. Hou, Wenbing & Pan, Qiuhui & He, Mingfeng, 2016. "A new graphical representation of protein sequences and its applications," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 444(C), pages 996-1002.
    8. Li, Yushuang & Liu, Qian & Zheng, Xiaoqi, 2016. "DUC-Curve, a highly compact 2D graphical representation of DNA sequences and its application in sequence alignment," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 456(C), pages 256-270.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:phsmap:v:409:y:2014:i:c:p:87-96. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.