ISSN : 2488-8648
International Journal of Basic Science and Technology
A publication of the Faculty of Science, Federal University Otuoke, Bayelsa State
Home About IJBST For Authors Issues Useful Downloads Contact
ISSN : 2488-8648
Home About IJBST For Authors Issues Useful Downloads Contact
Questions are asked and these questions need answers. This is the reason why this page is created to enable us share few worries!
×published date:2023-Oct-04
FULL TEXT in - 
| page 178 - 188
Abstract
Manual analysis of gel electrophoresis images is a significant research barrier and due to significant constraints, digital technologies have been applied to accelerate the processing and interpretation of gel images. This study aimed to evaluate DNA polymorphism in selected animal and environmental microbes using a manual and computational program for the gel image analysis. To ascertain and compare the accuracy of the analysis performed manually and computationally, Random amplified polymorphic DNA-PCR (RAPD-PCR) was performed, and gel electrophoresis was run on PCR products obtained from Staphylococcus spp cultured from livestock nasal swabs and Bacillus spp cultured from soil and wastewater samples from different abattoirs in Ogun State, Nigeria. Gel image analysis was done manually and computationally with two software programs, PyElph and GelAnalyzer. Results obtained from both analyses were compared, and some discrepancies were observed as the computerized analysis was not in total concordance with the manual visual analysis. The software programs were compared using several parameters: image quality enhancement, visual band, lane detection and definition, data clustering, and dendrogram analysis. PyElph had approximately 60% accuracy in all the features tested, although when compared to manual gel visualization for bands and lanes calculation; there was an inaccuracy with PyElph while GelAnalyzer had a lower percentage of accuracy and lesser functionalities. This research has comprehensively analyzed the most commonly used noncommercial software programs available to researchers and students. This will help identify the features that need to be modified to develop a more effective system for the computational analysis of gel images
Keywords: RAPD, Image Analysis, Nigeria, Manual, Polymorphism
References
Abeykoon, A., Dhanapala, M., Yapa, R. and Sooriyapathirana, S. (2015). An automated system for analyzing agarose and polyacrylamide gel images. Ceylon Journal of Science (Biological Sciences), 44(1): 45-54.
Ahmed, N. (2021). EgyGene GelAnalyzer4: a powerful image analysis software for one dimensional gel electrophoresis. Journal of Genetic Engineering and Biotechnology, 19(1): 18-20.
Alnamoly, M., Alzohairy, A. and El-Henawy, I. (2020). EGBIOIMAGE: A Software Tool for Gel Images Analysis and Hierarchical Clustering. IEEE Access, 8(1): 10768-10781.
Chatterjee, S. and Raval, I. (2019). Pathogenic Microbial Genetic Diversity with Reference to Health. Microbial Diversity in the Genomic Era, 2(1): 559-577.
Dashti, N., Khanafer, M., El-Nemr, I., Sorkhoh, N., Ali, N. and Radwan, S. (2009). The potential of oil-utilizing bacterial consortia associated with legume root nodules for cleaning oily soils. Chemosphere, 74(10): 1354-1359.
Heras, J., Dominguez, C., Mata, E., Pascual, V., Lozano, C., Torres, C. and Zarazaga, M. (2016). A survey of tools for analysing DNA fingerprints. Briefings in Bioinformatics,17(6): 903-911.
Kaabouch, N., Schultz, R., Milavetz, B. and Balakrishnan, L. (2007). An analysis system for DNA gel electrophoresis images based on automatic thresholding and enhancement. IEEE International Conference on Electro/Information Technology, pp 26-31.
Khakabimamaghani, S., Najafi, A., Ranjbar, R. and 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.
Labyed, Y., Kaabouch, N., Schultz, R., Singh, B. and Milavetz, B. (2010). An Improved 1-D Gel Electrophoresis Image Analysis System. Advances in Experimental Medicine and Biology, 680: 609-617.
Maramis, C. and Delopoulos, A. (2010). Efficient Quantitative Information Extraction from PCRRFLP Gel Electrophoresis Images. Proceedings of the 2010 20th International Conference on Pattern Recognition, 2(1): 2560–2563.
Pavel, A. and Vasile, C. (2012). PyElph - a software tool for gel images analysis and phylogenetics. BMC Bioinformatics, 13(1): 40-49.
Rementeria, A., Gallego, L., Quindos, G. and Garaizar, J. (2001). Comparative evaluation of three commercial software packages for analysis of DNA polymorphism patterns. Clinical Microbiology and Infection, 7(6): 331-336.
FULL TEXT in - | page 178 - 188
Issue 3-Jul-Sep
Issue 2-Apr-Jun
Issue 1-Jan-Mar
Issue 4-Oct-Dec
Issue 3-Jul-Sep
Issue 2-Apr-Jun
Issue 1-Jan-Mar
Issue 4-Oct-Dec
Issue 3-Jul-Sep
Issue 2-Apr-Jun
Issue 1-Jan-Mar
Issue 4-Oct-Dec
Issue 2-Apr-Jun
Issue 1-Jan-Mar
Issue 4-Oct-Dec
Issue 3-Jul-Sep
Issue 4-Oct-Dec
Issue 2-Apr-Jun
Issue 1-Jan-Mar
Issue 4-Oct-Dec
Issue 3-Jul-Sep
Issue 2-Apr-Jun
Issue 4-Oct-Dec
Issue 1-Jan-Mar
Copyright © International Journal of Basic Science and Technology | Faculty of Science, Federal University Otuoke 2019. All Rights Reserved.
P.M.B. 126, Yenagoa. Bayelsa state Nigeria
Get the most recent updates
and be updated your self...