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凝胶分析及系统发育树整合工具:PyElph - a software tool for gel images analysis and phylogenetics  

2012-08-10 16:58:35|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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凝胶分析及系统发育树整合工具:PyElph - a software tool for gel images analysis and phylogenetics - 喜欢吃桃子 - wangyufeng的博客
 Figure 1. PyElph GUI - the band matching step. The figure is a screen capture of PyElph band matching step. Lanes, bands and band matching can be observed in the figure, as well as some GUI components, the toolbar, the options panel for the current step and the image view.

Background

This paper presents PyElph, a software tool which automatically extracts data from gel images, computes the molecular weights of the analyzed molecules or fragments, compares DNA patterns which result from experiments with molecular genetic markers and, also, generates phylogenetic trees computed by five clustering methods, using the information extracted from the analyzed gel image. The software can be successfully used for population genetics, phylogenetics, taxonomic studies and other applications which require gel image analysis. Researchers and students working in molecular biology and genetics would benefit greatly from the proposed software because it is free, open source, easy to use, has a friendly Graphical User Interface and does not depend on specific image acquisition devices like other commercial programs with similar functionalities do.

Results

PyElph software tool is entirely implemented in Python which is a very popular programming language among the bioinformatics community. It provides a very friendly Graphical User Interface which was designed in six steps that gradually lead to the results. The user is guided through the following steps: image loading and preparation, lane detection, band detection, molecular weights computation based on a molecular weight marker, band matching and finally, the computation and visualization of phylogenetic trees. A strong point of the software is the visualization component for the processed data. The Graphical User Interface provides operations for image manipulation and highlights lanes, bands and band matching in the analyzed gel image. All the data and images generated in each step can be saved. The software has been tested on several DNA patterns obtained from experiments with different genetic markers. Examples of genetic markers which can be analyzed using PyElph are RFLP (Restriction Fragment Length Polymorphism), AFLP (Amplified Fragment Length Polymorphism), RAPD (Random Amplification of Polymorphic DNA) and STR (Short Tandem Repeat). The similarity between the DNA sequences is computed and used to generate phylogenetic trees which are very useful for population genetics studies and taxonomic classification.

Conclusions

PyElph decreases the effort and time spent processing data from gel images by providing an automatic step-by-step gel image analysis system with a friendly Graphical User Interface. The proposed free software tool is suitable for researchers and students which do not have access to expensive commercial software and image acquisition devices.

Availability and Requirements

? Project name: PyElph

? Project home page: http://sourceforge.net/projects/pyelph/files/releases/ webcite

? Operating system(s): Platform independent

? Programming language: Python 2.x

? Other requirements: Python 2.5 or higher, Numpy, PIL (Python Image Library), wxPython, matplotlib

? License: GNU GPL v3

? Any restrictions to use by non-academics: restrictions specified by GNU GPL v3

Before the application can be started, the following open source Python packages must be installed:

1. Python 2.5 or 2.6 interpreter - http://python.org/download/releases/ webcite

2. The following Python packages for Python 2.5 or 2.6:

(a) Numpy - http://numpy.scipy.org webcite or http://sourceforge.net/projects/numpy/files/NumPy/ webcite

(b) PIL - http://www.pythonware.com/products/pil/ webcite

(c) wxPython - http://www.wxpython.org webcite or http://sourceforge.net/projects/wxpython/files/wxPython/ webcite

(d) Matplotlib - http://matplotlib.sourceforge.net webcite or http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.0/ webcite

After instalation of the required packages is ready, PyElph can be started by double-clicking on PyElph.py python script. The folder standards contained the defined weight marker standards. New weight marker stadards can be defined and saved from PyElph GUI or by editing a text file with the .marker extension.

For the convenience of Windows users, an installation kit is also available at http:/ / sourceforge.net/ projects/ pyelph/ files/ releases/ PyElph1.3-installer.exe/ download webcite. The kit installs a windows executable version of PyElph, which was generated with py2exe. Therefore, there is no need to install Python or other python packages to run this executable version of PyElph.

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