Fully-Automated Spot Recognition and Matching Algorithms for 2-D Gel Electrophoretogram of Genomic DNA

Katsutoshi Takahashi[1] (sltaka@jaist.ac.jp)
Masayuki Nakazawa[2] (nakazawa@ishikawa-pc.ac.jp)
Yasuo Watanabe[3] (watanabe@infor.kanazawa-it.ac.jp)
Akihiko Konagaya[1] (kona@jaist.ac.jp)

[1] Japan Advanced Institute of Science and Technology (JAIST) Hokuriku
Asahidai 1, Tatsunokuchi, Ishikawa 923-1211, Japan
[2] Ishikawa Polytechnic College
Yuigaoka I 45-1, Anamizu, Ishikawa 927-0024, Japan
[3] Kanazawa Institute of Technology
Ohgigaoka 7-1, Nonoichi, Ishikawa 921-8501, Japan


Abstract

We have developed the fully-automated algorithms for processing 2-D gel electrophoretograms based on RLGS (restriction landmark genomic scanning) method; one for fully-automated spot recognition from RLGS electrophoretogram and another for fully-automated pairwise matching of the spots found on such 2-D electrophoretograms. Without any human interaction, several thousands of spots on a 2-D electrophoretogram, including hidden spots found at the shoulder of large spots, can be identified correctly by applying our spot recognition algorithm, except for only a few true-negative and false-positive spots. Once the locations and intensities of the landmark spots are correctly recognized automatically, our pairwise spot matching algorithm reliably and rapidly identifies equivalent pairs of spots found on the nonlinearly distorted RLGS electrophoretograms in the fully-automatic way, i.e., the boring and annoying spot landmarking process is unnecessary. At the beginning of the spot matching process, most suitable pair of corresponding spots is searched automatically, then the other equivalent pairs of spots are identified. With our powerful image processing algorithms, it is possible to detect DNA molecular changes such as deletions, additions, amplifications or DNA methylations occurring at or near to the restriction enzyme cleavage sites by means of comparing large amount of RLGS electrophoretograms, without any visual inspection and human interaction.

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Japanese Society for Bioinformatics