Analyse-Tools zur Verwendung bei Gelelektorphorese
|Titel||Analyse-Tools zur Verwendung bei Gelelektorphorese|
|Institution||Fachhochschul-Bachelorstudiengang Medizin- und Bioinformatik|
A common way for separating DNA, RNA or proteins by their mass or length is the use of agarose- or polyacrylamide-gels. There are several fields in which gel electrophoresis is used, like DNA fingerprinting, medical diagnostics, parentage testing, forensics, etc. (Heras, et al., 2015)
An image or scan of the gel can be analysed by hand/ruler or by using a tool created for such an analysis. In order to analyse the picture, the bands need to be cut and orientated. Some tools additionally allow the user to adjust the brightness, contrast and other values to increase the visibility of the bands.
As soon as the picture has been prepared for the analysis, lanes and bands are defined and known values for the markers are recorded. For each band of a non-reference-lane a band in the reference lane (containing the markers) is matched, so the mass or length of the non-reference band can be approximated.
For this thesis I created a tool for analysing gel-electrophoresis images, compared the newly created tool with existing applications and contrasted their characteristics as well as the workflow.
With the implemented tool the user can load an image and adjust its contrast and brightness to increase the visibility of the bands. In the loaded image the user can set and delete a starting line, the lanes and the bands and define in which lane the reference is located. Additionally, the user can type in values for the marker and save the input or load previously defined markers. When the analysis is complete, a CSV-file can be created, which contains the values of the marker, its unit and the bands with their distance to the starting line. Opening the file in Microsoft Excel or a similar program allows the user to create a scatterplot, which includes he marker-values as x-axis and the distances of the bands as y-axis-values.