title: Geometric algorithms for the analysis of 2D-electrophoresis gels.
abstract: In proteomics, two-dimensional gel electrophoresis (2-DE) is a separation technique for proteins. The resulting protein spots can be identified either by 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 related theoretical questions in computational geometry.
authors.affiliation: Computer Science Department, University of Arizona, Tucson, AZ 85721-0077, USA.
authors.forename: Alon
authors.initials: A
authors.lastname: Efrat
authors.forename: Frank
authors.initials: F
authors.lastname: Hoffmann
authors.forename: Klaus
authors.initials: K
authors.lastname: Kriegel
authors.forename: Christof
authors.initials: C
authors.lastname: Schultz
authors.forename: Carola
authors.initials: C
authors.lastname: Wenk
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D015180:Electrophoresis, Gel, Two-Dimensional / Q000706:statistics & numerical data*; D007091:Image Processing, Computer-Assisted / Q000706:statistics & numerical data; D011506:Proteins / Q000235:genetics / Q000302:isolation & purification*; D020543:Proteome; D012984:Software; D012985:Software Design
chemical_list: D011506:Proteins; D020543:Proteome