Geometric algorithms for the analysis of 2D-electrophoresis gels

A. Efrat, F. Hoffmann, K. Kriegel, C. Schultz, C. Wenk

Research output: Contribution to conferencePaper

12 Scopus citations

Abstract

In proteomics 2-dimensional gel electrophoresis (2-DE) is a separation technique for proteins. The resulting protein spots can be identified by either using picking robots and subsequent mass spectrometry or by visual cross inspection of a new gel image with an already analyzed master gel. Difficulties especially arise from inherent noise and irregular geometric distortions in 2-DE images. Aiming at the automated analysis of large series of 2-DE images, or at the even more difficult interlaboratory gel comparisons, the bottleneck is to solve the two most basic algorithmic problems with high quality: Identifying protein spots and computing a matching between two images. For the development of the analysis software CAROL at Freie Universität Berlin we have reconsidered these two problems and obtained new solutions which rely on methods from computational geometry. Their novelties are: 1. Spot detection is also possible for complex regions formed by several "merged" (usually saturated) spots; 2. User-defined landmarks are not necessary for the matching. Furthermore, images for comparison are allowed to represent different parts of the entire protein pattern, which only partially "overlap". The implementation is done in a client server architecture to allow queries via the Internet. We also discuss and point at rela ted theoretical questions in computational geometry.

Original languageEnglish (US)
Pages114-123
Number of pages10
DOIs
StatePublished - 2001
Event5th Annual Internatinal Conference on Computational Biology - Montreal, Que., Canada
Duration: May 22 2001May 26 2001

Other

Other5th Annual Internatinal Conference on Computational Biology
CountryCanada
CityMontreal, Que.
Period5/22/015/26/01

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)

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    Efrat, A., Hoffmann, F., Kriegel, K., Schultz, C., & Wenk, C. (2001). Geometric algorithms for the analysis of 2D-electrophoresis gels. 114-123. Paper presented at 5th Annual Internatinal Conference on Computational Biology, Montreal, Que., Canada. https://doi.org/10.1145/369133.369181