ANALYSIS OF MICROBIOME SEQUENCES USING MOTHUR
DOI:
https://doi.org/10.24867/03BE05KantarKeywords:
16S rRNA, classification, microbiome, MothurAbstract
In this paper 16S rRNA microbiome sequences were analized using Mothur pipeline for their further classification based on the obtained taxonomic description. Classification is performed using random forest algorithm achieveing accuracy of 95,46%. The results were discussed and compared with the previous findings from the literature.
References
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[2] P. D. Schloss, et al. "Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities", Applied and environmental microbiology 75.23, p.7537-7541, 2009.
[3] https://www.arb-silva.de/documentation/release-132/ (pristupljeno u septembru 2018.)
[4] J. G. Caporaso, C. L. Lauber, E. K. Costello, D. Berg-Lyons, A. Gonzalez, J. Stombaugh, D. Knights, P. Gajer, J. Ravel, N. Fierer et al., "Moving pictures of the human microbiome," Genome Biol, vol. 12, no. 5, 2011.
[5] http://qiime.org/ (pristupljeno u septembru 2018.)
[6] E. Plummer, et al., "A comparison of three bioinformatics pipelines for the analysis of preterm gut microbiota using 16S rRNA gene sequencing data," Journal of Proteomics & Bioinformatics, 8.12: 283, 2015.
[7] http://greengenes.secondgenome.com/ (pristupljeno u oktobru 2018.)
[8] T. K. Ho, "Random decision forests," Document analysis and recognition, proceedings of the third international conference on. vol. 1. IEEE, 1995.
[9] G. James, et al., "An introduction to statistical learning, " New York: springer, 2013.
[10] D. Pavlović, "Stabilna procena klastera konsenzus klasterovanjem uzoraka mikrobioma", Diplomski rad, Fakultet tehničkih nauka, Novi Sad, 2017.
[11] S. Brdar, T. Lončar-Turukalo, V. Crnojević, B. Stres, "Clustering and classification of human microbiome data: evaluating impact of different settings in bioinformatics workflows," Book of Abstracts of the second Belgrade BioInformatics Conference – BelBi 2018, in Biologia Serbica, vol. 40, No1, 2018, pp. 67 Belgrade, June, 18-22, 2018.
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Published
2019-05-22
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Section
Electrotechnical and Computer Engineering
