Volume 7, Issue 1, June 2019, Page: 1-4
Transcription Direction Patterns of Adjacent Genes in Mycobacterium Tuberculosis Using GENAVIS
Angela Uche Makolo, Department of Computer Science, University of Ibadan, Ibadan, Nigeria
Received: Feb. 2, 2019;       Accepted: Mar. 22, 2019;       Published: Apr. 18, 2019
DOI: 10.11648/j.cbb.20190701.11      View  264      Downloads  50
Abstract
The understanding of the relationship of a gene with other genes in its neighbourhood and the implication of this relationship on the biochemical activities of the entire genome need an efficient computational tool to unfold the relationship. GENAVIS: (GENe Adjacency VIsualization Software) is an open source, platform independent web-based software for modeling neighborhood genes as binary codes. We also incorporated the feature of having an interactive visual representation of patterns of the binary code for a specific gene family in multiple microbial genomes. The concept of using binary code for representation is derived from computational thinking techniques which models problems using computer logic of applying abstraction and pattern matching to extract hidden patterns aimed at knowledge discovery. The result provides an insight into the analysis of transcriptional unit with more than one gene and genes encoding for universal stress protein, which also allows for a comparative analysis of multiple genomes as the basis for biosynthetic pathways and multi-gene function prediction.
Keywords
Neighbourhood, Adjacency, Transcription Direction, Universal Stress Protein, Binary Code
To cite this article
Angela Uche Makolo, Transcription Direction Patterns of Adjacent Genes in Mycobacterium Tuberculosis Using GENAVIS, Computational Biology and Bioinformatics. Vol. 7, No. 1, 2019, pp. 1-4. doi: 10.11648/j.cbb.20190701.11
Copyright
Copyright © 2019 Authors retain the copyright of this article.
This article is an open access article distributed under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Reference
[1]
B. C. Resendea, A. B. Rebelatoa, V. D'Afonsecab, A. R. Santos b, T. Stutzmanb, V. A. Azevedob, L. L. Santos A, A. Miyoshi B, D. O. Lopes. DNA repair in Corynebacterium model. Gene 2011 482: 1-7.
[2]
Baraka S. Williams, Raphael D. Isokpehi, Andreas N. Mbah, Antoinesha L. Hollman, Christina O. Bernard, 1Shaneka S. Simmons, Wellington K. Ayensu, and Bianca L. Garner. Functional Annotation Analytics of Bacillus Genomes Reveals Stress Responsive Acetate Utilization and Sulfate Uptake in the Biotechnologically Relevant Bacillus megaterium. BioinformBiol Insights. 2012; 6:275-86. doi: 10.4137/BBI.S7977. Epub 2012 Nov 21.
[3]
Chen Y., Zhang Z., Zheng J., Maa Y. and Xue Y. (2017). Gene selection for tumor classification using neighborhood rough sets and entropy measures. Journal of Biomedical Informatics 67 (2017) 59–68. http://dx.doi.org/10.1016/j.jbi.2017.02.007.
[4]
Hou M., Wang S., Li X. and Lei Y. (2009). Neighborhood Rough Set Reduction-Based Gene Selection and Prioritization for Gene Expression Profile Analysis and Molecular Cancer Classification. Journal of Biomedicine and Biotechnology. Volume 2010, Article ID 726413, 12 pages doi:10.1155/2010/726413.
[5]
Jiang W., Sun l., Yang X., Wang M., Esmaeili N., Pehlivan N., Zhao R., Zhang H. and Zhao Y. (2017). The Effects of Transcription Directions of Transgenes and the gypsy Insulators on the Transcript Levels of Transgenes in Transgenic Arabidopsis. Scientific Reports | 7: 14757 | DOI:10.1038/s41598-017-15284-x.
[6]
Jones R (2010) There Goes the (Gene Expression) Neighbourhood Theory. PLoS Biol 8(11): e1001002. doi:10.1371/journal.pbio.1001002.
[7]
L. Martinez-Martinez et al., Clinical significance of Corynebacterium striatum isolated from human sample, Clin Microbiol Infect. 1997 Feb; 3(6):634-639.
[8]
Larkin J. D., Cook P. R., and Papantonis A. (2012). Dynamic Reconfiguration of Long Human Genes during One Transcription Cycle. Molecular and Cellular Biology. Volume 32 Number 14. p. 2738–2747.
[9]
Makolo Angela and Isokpehi Raphael (2015): Interactive Visual Representations of Gene Transcriptional Direction Patterns in Microbial Genomes. European Molecular Biology Organization Conference on Visualization of Biological Data, VISBI 2015, USA. http://vizbi.org/Posters/2015/B10.
[10]
Oliver B., Parisi M. and Clark D. (2002). Gene expression neighborhoods. Journal of Biology 2002, Volume 1, Issue 1, Article 4. http://jbiol.com/content/1/1/4.
[11]
Srivatsan A, Tehranchi A, MacAlpine DM, Wang JD (2010) Co-Orientation of Replication and Transcription Preserves Genome Integrity. PLoS Genet 6(1): e1000810. doi:10.1371/journal.pgen.1000810.
[12]
Tremonte P., Succi M., Coppola R., Sorrentino E., Tipaldi L., Picariello G., Pannella G. and Fraternali F. (2016) Homology-Based Modeling of Universal Stress Protein from Listeria innocua Up-Regulated under Acid Stress Conditions. Front. Microbiol.7:1998. doi: 10.3389/fmicb.2016.01998.
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