1
Computer Science Department, Faculty of Computers and Informatics, Zagazig University
(mahmoudalnamoly2014@gmail.com)
2
Genetics Department, Faculty of agriculture, Zagazig University
(amansour@zu.edu.eg)
3
Computer Science Department, Faculty of Computers and Informatics, Zagazig University, Egypt
(ielhenawy@zu.edu.eg)
Abstract :
One of the most severe sources of information for a molecular biologist is the gel image generated by using gel electrophoresis during the experiment of issr-pcr, sds-pages, and rapd-pcr. DNA and protein gel images are obtained through the gel electrophoresis separations techniques of DNA and protein fragments. The separation of the polymorphic bands is based on the sizes of the negatively charged DNA fragments running from the negative cathode toward the positive anode. Each gel image has some vertical lanes; each lane corresponds to one sample and has several horizontal bands. The resulting images produced by Gel electrophoresis are sometimes difficult to interpret so that it was important to develop software tools to analyze the gel images to help biologists in the process of analyzing gel image as they draw their conclusions according to the results that generated from gel image analyzer software. In this article, we present a survey of some commercial and non-commercial software tools that are used for analyzing gel images. We develop a novel software for processing and analyzing the gel electrophoresis images, computing the molecular weights, saving them as excel sheet, clustering the bands based on their molecular weights using k-means algorithm, Applying band matching using a tolerance value entered by the user, determine the similarities between samples, drawing the corresponding phylogenetic tree, saving a report of the experiment as a pdf, and printing this report. The novel software will provide the biologist with the ability of manual processing, automatic processing, and semi-automatic processing.
Keywords :
Gel electrophoresis images; Phylogenetic tree; software tools
References :
[1] Kaabouch, N., Schultz, R. R., Milavetz, B., & Balakrishnan, L. (2007, May). An analysis system for DNA gel electrophoresis images based on automatic thresholding an enhancement. In 2007 IEEE International Conference on Electro/Information Technology (pp. 26-31). IEEE.
[2] Kaufmann, M. E., & Pitt, T. L. (2018). Pulsed-field gel electrophoresis of bacterial DNA. In Methods in practical laboratory bacteriology (pp. 83-92). CRC Press.
[3] Heras, J., Domínguez, C., Mata, E., Pascual, V., Lozano, C., Torres, C., & Zarazaga, M. (2015). GelJ–a tool for analyzing DNA fingerprint gel images. BMC bioinformatics, 16(1), 270.
[4] Lin, C. Y., Ching, Y. T., & Yang, Y. L. (2007). Automatic method to compare the lanes in gel electrophoresis images. IEEE Transactions on information technology in biomedicine, 11(2), 179-189.
[5] Murchan, S., Kaufmann, M. E., Deplano, A., de Ryck, R., Struelens, M., Zinn, C. E., ... & Cuny, C. (2003). Harmonization of pulsed-field gel electrophoresis protocols for epidemiological typing of strains of methicillin-resistant Staphylococcus aureus: a single approach developed by consensus in 10 European laboratories and its application for tracing the spread of related strains. Journal of clinical microbiology, 41(4), 1574-1585.
[6] Heras, J., Domínguez, C., Mata, E., Pascual, V., Lozano, C., Torres, C., & Zarazaga, M. (2015). A survey of tools for analysing DNA fingerprints. Briefings in bioinformatics, 17(6), 903-911.
[7] Ferreira, T., & Rasband, W. (2012). ImageJ user guide. ImageJ/Fiji, 1, 155-161.
[8] Pavel, A. B., & Vasile, C. I. (2012). PyElph-a software tool for gel images analysis and phylogenetics. BMC bioinformatics, 13(1), 9.
[9] Khakabimamaghani, S., Najafi, A., Ranjbar, R., & Raam, M. (2013). GelClust: a software tool for gel electrophoresis images analysis and dendrogram generation. Computer methods and programs in biomedicine, 111(2), 512-518.
[10] Alawdi, R. M., Amer, R. B., Alzohairy, A. M., & Khedr, W. M. The Computational Techniques Developed to Analyze DNA Gel Images. International Journal of Advanced Engineering Research and Science, 3(7).
| Style | # |
|---|---|
| MLA | Mahmoud H.Alnamoly, Ahmed M. Alzohairy, Ibrahim M. El-Henawy. "A survey on gel images analysis software tools." Journal of Intelligent Systems and Internet of Things, Vol. 1, No. 1, 2021 ,PP. 40-47 (Doi : https://doi.org/10.54216/JISIoT.010103) |
| APA | Mahmoud H.Alnamoly, Ahmed M. Alzohairy, Ibrahim M. El-Henawy. (2021). A survey on gel images analysis software tools. Journal of Journal of Intelligent Systems and Internet of Things, 1 ( 1 ), 40-47 (Doi : https://doi.org/10.54216/JISIoT.010103) |
| Chicago | Mahmoud H.Alnamoly, Ahmed M. Alzohairy, Ibrahim M. El-Henawy. "A survey on gel images analysis software tools." Journal of Journal of Intelligent Systems and Internet of Things, 1 no. 1 (2021): 40-47 (Doi : https://doi.org/10.54216/JISIoT.010103) |
| Harvard | Mahmoud H.Alnamoly, Ahmed M. Alzohairy, Ibrahim M. El-Henawy. (2021). A survey on gel images analysis software tools. Journal of Journal of Intelligent Systems and Internet of Things, 1 ( 1 ), 40-47 (Doi : https://doi.org/10.54216/JISIoT.010103) |
| Vancouver | Mahmoud H.Alnamoly, Ahmed M. Alzohairy, Ibrahim M. El-Henawy. A survey on gel images analysis software tools. Journal of Journal of Intelligent Systems and Internet of Things, (2021); 1 ( 1 ): 40-47 (Doi : https://doi.org/10.54216/JISIoT.010103) |
| IEEE | Mahmoud H.Alnamoly, Ahmed M. Alzohairy, Ibrahim M. El-Henawy, A survey on gel images analysis software tools, Journal of Journal of Intelligent Systems and Internet of Things, Vol. 1 , No. 1 , (2021) : 40-47 (Doi : https://doi.org/10.54216/JISIoT.010103) |