Ahmed N E
Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.
J Genet Eng Biotechnol. 2021 Jan 25;19(1):18. doi: 10.1186/s43141-020-00114-x.
Gel image analysis is a cornerstone in electrophoresis-based experiments. Nature of the experiment determines the target of the analysis. Implemented features within different software for gel images and their outputs are variable. EgyGene GelAnalyzer4 software aimed to make a powerful, easy, and almost all-in-one software for gel image analysis.
EgyGene GelAnalyzer4 is a software for analyzing the gel images. The program consists of six main parts: gel image enhancement, image analysis, data merging, molecular markers detection, phylogenetic tree prediction, and population parameters estimation. Firstly, the gel image enhancement part enhances the gel image colors and clarity. Then, the image is analyzed in the second part using both automatic and manual detection of lanes and bands. The third part, data merging, is for merging several analyses for different samples/gels together to produce one table comprises the entire experiment. The fourth section, markers detection, collects several pre-analyzed data for the same samples to detect their molecular markers based on some user-defined criteria. The fifth part uses the outputs of the previous parts to draw the phylogenetic tree between samples. The program constructs a phylogenetic tree using unweighted pair group method with arithmetic mean (UPGMA) method. Fourteen different equations are used to calculate the similarity percentages: Anderberg, Czekanowski, Dice, Faith, Gower and Legendre, Jaccard, Nei and Li, Rogers and Tanimoto, Russel and Rao, simple matching, Sokal and Michener, Sokal and Sneath 1, Sokal and Sneath 2, and Sorensen. The last section calculates the population parameters for the pre-analyzed images before. EgyGene GelAnalyzer4 is designed and programed using Microsoft Visual Studio 2012 Express version, based on the Dot Net FrameWork 4.5 edition, whereas its icons are created using the freeware Greenfish Icon Editor Pro 3.2.5.1.
EgyGene GelAnalyzer4 is a simple, fast, and user-friendly software with six novel features: changing the order of lanes within the gel image, splitting the detecting lane into two lanes, merging of several detected lanes into just one, splitting a single band into two bands, merging two or more bands to be a single band, and comparing data of several analyzed images with a big number of samples and merging it together in a single table and detection of molecular markers between samples. In addition to the basic features and outputs of other image analysis software such as calculation of relative mobility values, molecular weights/sizes estimation, DNA/RNA/protein quantity within bands, table of present/absent of bands, polymorphism percentage, similarity percentages and phylogeny, population parameters, enhancing the image colors and clarity, and merging data for several gels. In addition, writing names of samples and the detected markers on the image. EgyGene GelAnalyzer4 provides many several features, which may be not available together in any other alternative.
凝胶图像分析是基于电泳实验的基石。实验性质决定了分析的目标。不同凝胶图像软件所实现的功能及其输出各不相同。EgyGene GelAnalyzer4软件旨在打造一款功能强大、操作简便且几乎集所有功能于一体的凝胶图像分析软件。
EgyGene GelAnalyzer4是一款用于分析凝胶图像的软件。该程序由六个主要部分组成：凝胶图像增强、图像分析、数据合并、分子标记检测、系统发育树预测和群体参数估计。首先，凝胶图像增强部分可增强凝胶图像的颜色和清晰度。然后，在第二部分中使用自动和手动检测泳道和条带的方式对图像进行分析。第三部分，数据合并，用于将针对不同样品/凝胶的多个分析合并在一起，以生成一个包含整个实验的表格。第四部分，标记检测，收集针对相同样品的多个预先分析的数据，以便根据一些用户定义的标准检测其分子标记。第五部分使用前几部分的输出结果绘制样品之间的系统发育树。该程序使用算术平均的非加权组对法（UPGMA）构建系统发育树。使用14种不同的方程来计算相似百分比：安德伯格方程、切卡诺夫斯基方程、迪西方程、费思方程、高尔方程和勒让德方程、雅卡尔方程、内和李方程、罗杰斯和谷本方程、拉塞尔和饶方程、简单匹配方程、索卡尔和米切纳方程、索卡尔和斯内斯1方程、索卡尔和斯内斯2方程以及索伦森方程。最后一部分计算之前预先分析图像的群体参数。EgyGene GelAnalyzer4是使用Microsoft Visual Studio 2012 Express版本基于Dot Net FrameWork 4.5版本设计和编程的，而其图标是使用免费软件Greenfish Icon Editor Pro 3.2.5.1创建的。
EgyGene GelAnalyzer4是一款简单、快速且用户友好的软件，具有六个新颖的功能：改变凝胶图像中泳道的顺序、将检测泳道拆分为两个泳道、将多个检测到的泳道合并为一个、将单个条带拆分为两个条带、将两个或多个条带合并为一个条带、比较多个分析图像的数据以及大量样品的数据并将其合并到一个表格中，以及检测样品之间的分子标记。除了其他图像分析软件的基本功能和输出，如相对迁移率值的计算、分子量/大小估计、条带内的DNA/RNA/蛋白质数量、条带存在/缺失表格、多态性百分比、相似百分比和系统发育、群体参数、增强图像颜色和清晰度以及合并多个凝胶的数据之外。此外，还可以在图像上写入样品名称和检测到的标记。EgyGene GelAnalyzer4提供了许多其他软件可能无法同时具备的功能。
