title: Automatic analysis of 2D polyacrylamide gels in the diagnosis of DNA polymorphisms.
abstract: BACKGROUND
  The analysis of polyacrylamide gels is currently carried out manually or automatically. In the automatic method, there are limitations related to the acceptable degree of distortion of lane and band continuity. The available software cannot deal satisfactorily with this type of situations. Therefore, the paper presents an original image analysis method devoid of the aforementioned drawbacks.
  
  
  METHODS
  This paper examines polyacrylamide gel images from Li-Cor DNA Sequencer 4300S resulting from the use of the electrophoretic separation of DNA fragments. The acquired images have a resolution dependent on the length of the analysed DNA fragments and typically it is MG×NG=3806×1027 pixels. The images are saved in TIFF format with a grayscale resolution of 16 bits/pixel. The presented image analysis method was performed on gel images resulting from the analysis of DNA methylome profiling in plants exposed to drought stress, carried out with the MSAP (Methylation Sensitive Amplification Polymorphism) technique.
  
  
  RESULTS
  The results of DNA polymorphism analysis were obtained in less than one second for the Intel Core™ 2 Quad CPU Q9300@2.5GHz, 8GB RAM. In comparison with other known methods, specificity was 0.95, sensitivity = 0.94 and AUC (Area Under Curve) = 0.98.
  
  
  CONCLUSIONS
  It is possible to carry out this method of DNA polymorphism analysis on distorted images of polyacrylamide gels. The method is fully automatic and does not require any operator intervention. Compared with other methods, it produces the best results and the resulting image is easy to interpret. The presented method of measurement is used in the practical analysis of polyacrylamide gels in the Department of Genetics at the University of Silesia in Katowice, Poland.
authors.affiliation: Department of Biomedical Computer Systems, Institute of Computer Science, University of Silesia, Będzińska 39, 41-200, Sosnowiec, Poland. robert.koprowski@us.edu.pl
authors.forename: Robert
authors.initials: R
authors.lastname: Koprowski
authors.forename: Zygmunt
authors.initials: Z
authors.lastname: Wróbel
authors.forename: Anna
authors.initials: A
authors.lastname: Korzyńska
authors.forename: Karolina
authors.initials: K
authors.lastname: Chwiałkowska
authors.forename: Mirosław
authors.initials: M
authors.lastname: Kwaśniewski
mesh_terms: D001331:Automation; D004247:DNA / Q000235:genetics* / Q000302:isolation & purification*; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods*; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA