• DocumentCode
    2872038
  • Title

    PMMR: A Method for Masking Repeats in DNA Fragment Assembly

  • Author

    Cai, Kui ; Yang, Jincai

  • Author_Institution
    Dept. of Econ. & Manage., Wuhan Univ. of Technol., Wuhan, China
  • Volume
    2
  • fYear
    2009
  • fDate
    18-19 July 2009
  • Firstpage
    11
  • Lastpage
    14
  • Abstract
    A method named PMMR (previously merging for masking repeats) is proposed in this paper for masking repeats in DNA fragment assembly. The method firstly identifies and counts the fragments including a same k-mer substring by scanning the shotgun data set. Then, it merges these fragments by the same k-mer substring. Based on merging, the method can not only mark the position of the repeats, but also reduce the scale of shotgun data set. The computer simulations show that the rate of repeats recognition is enhanced in this method, and the CPU time of DNA fragment assembly will be reduced.
  • Keywords
    DNA; biocomputing; string matching; CPU time; DNA fragment assembly; k-mer substring; previously merging for masking repeats; repeats recognition; shotgun data set; Assembly; DNA; Information processing; fragment assembly; k-mer substring; masking repeats; previously merging;
  • fLanguage
    English
  • Publisher
    ieee
  • Conference_Titel
    Information Processing, 2009. APCIP 2009. Asia-Pacific Conference on
  • Conference_Location
    Shenzhen
  • Print_ISBN
    978-0-7695-3699-6
  • Type

    conf

  • DOI
    10.1109/APCIP.2009.139
  • Filename
    5197124
    • Link To Document
    https://search.isc.ac/dl/search/defaultta.aspx?DTC=49&DC=2872038