Automatic analysis of 2D polyacrylamide gels in the diagnosis of DNA polymorphisms
PBN-AR
Instytucja
Instytut Biocybernetyki i Inżynierii Biomedycznej im. Macieja Nałęcza Polskiej Akademii Nauk
Informacje podstawowe
Główny język publikacji
en
Czasopismo
Biomedical Engineering Online
ISSN
1475-925X
EISSN
Wydawca
BIOMED CENTRAL LTD
DOI
URL
Rok publikacji
2013
Numer zeszytu
1
Strony od-do
68
Numer tomu
12
Identyfikator DOI
Liczba arkuszy
Streszczenia
Język
en
Treść
INTRODUCTION: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.MATERIAL: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 MGxNG=3806x1027 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 CoreTM 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.
Cechy publikacji
discipline:Biocybernetyka i inżynieria biomedyczna
discipline:Biocybernetics and biomedical engineering
Original article
Original article presents the results of original research or experiment.
Oryginalny artykuł naukowy
Oryginalny artykuł naukowy przedstawia rezultaty oryginalnych badań naukowych lub eksperymentu.
Inne
System-identifier
PBN-R:670257
CrossrefMetadata from Crossref logo
Cytowania
Liczba prac cytujących tę pracę
Brak danych
Referencje
Liczba prac cytowanych przez tę pracę
Brak danych