Comparing lanes in the Pulsed-Field Gel Electrophoresis (PFGE) images

Wei Zen Cheng*, Kue Sai Yen, Chih Yang Lin, Yu-Tai Ching, Yun Liang Yang

*Corresponding author for this work

Research output: Contribution to journalConference articlepeer-review

2 Scopus citations

Abstract

Pulsed-field Gel Electrophoresis (PFGE) is an important tool in genomic analysis. The result of PFGE is presented in an image. Each image contains several lanes. And each lane consists of bands. Two lanes are identical if the relative positions of bands are the same. We present a method that uses computer to extract the lanes and compare the lanes in the electrophoresis images. The presented method consists of two major steps. The first step is image processing and lane extraction. The second step is to convert a lane into chain code representation. The lane comparison is carried out through calculating the longest common subsequence between lanes. We define the distance between lanes in term of the LCS and the lengths of two lanes. Two lanes have smaller distance tend to have similar pattern. This method eliminates those very different patterns to help biologists reduce the lanes that need to be compared.

Original languageEnglish
Pages (from-to)2911-2913
Number of pages3
JournalAnnual Reports of the Research Reactor Institute, Kyoto University
Volume3
StatePublished - 1 Dec 2001
Event23rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Istanbul, Turkey
Duration: 25 Oct 200128 Oct 2001

Keywords

  • Chain code
  • Dynamic programming
  • Electrophoresis
  • Image processing

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