Abstract
This paper presents a novel software called EGBioImage that is implemented for analyzing gel Electrophoresis images, computing the molecular weights of the bands of the unknown size, detecting the types of the bands, grouping the bands according to their molecular weights and labeled each band with its group number in the gel image and generating the corresponding phylogenetic tree using the data extracted from the analyzed gel image. Students and Researchers working in molecular biology and genetics would benefit greatly from EGBioImage. This software is designed and developed under windows operating system using a C-sharp programming language. It uses Emgu CV platform to extract contours objects from an image that uses the green theorem to detect the bands in each detected lane. It uses polynomial regression to calculate the molecular weights of the bands of unknown size. It uses K-means clustering algorithm to cluster bands according to their molecular weights. It uses each of upgma algorithm and the matching bands amongst lanes and to construct the phylogenetic tree. EGBioImage provides a very friendly Graphical User Interface that guides the user from the step of uploading a gel image toward getting the molecular weights of the bands of unknown size and generating the Phylogenetic Tree. Moreover, EGBioImage provides the user with the ability of processing the gel image using a completely manual processing and automatic processing with the ability of manual correction of lanes and bands “Semi-automatic process” and it is more accurate than comparable software in some respects and the only software that divides the bands into groups and labeled them with numbers in the gel image based on their group by implementing k-means algorithm and these claims are supported with experiments. EGBioImage is suitable for students and researchers who do not have access to commercial software.
Highlights
Gel Electrophoresis (GE) is an important technique which widely used in the molecular biologist experiments to separate the DNA based on their size or weights and generating the DNA and protein gel images [1]
The gel image which produced from the gel electrophoresis on the experiments is one of the most important and essential sources of information for any molecular biologists as they draw their conclusions based on the results getting from analyzing the gel image
EGBioImage generates the phylogenetic tree unlike some other commercial software which does not generate phylogenetic such as EzQuant, Dolphin 1D, Gel-Pro Analyzer, Intelligent Quantifier, Molecular Imaging, myImage Analysis, Un-Scan-it, Gel-Quant, Image Lab, ImageStudio, LabImage and Ultraquant and some other non-commercial software such as Laneruler, GelAnalyzer, GelQuant and ImageJ
Summary
Gel Electrophoresis (GE) is an important technique which widely used in the molecular biologist experiments to separate the DNA based on their size or weights and generating the DNA and protein gel images [1]. The larger segments are run slower than smaller ones and staying in the upper position of the lanes so that bands on the upper of Lane is the larger, has the biggest weights and the smaller fragments migrate faster through the gel and occupy the lower position of the lanes. The separation process of the polymorphic bands is done based on the size of the DNA fragments which running form the negative cathode toward the positive anode. The smaller fragments of DNA migrate faster through the gel and occupy the lower position of the gel and The fragments of DNA with larger size will be appear on the top of the gel as it blocked from passing through the
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