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Simple approach to bacterial genomes comparison based on Average Nucleotide Identity (ANI) using fastANI and ANIclustermap

dc.contributor.authorMusiał, Klaudia
dc.contributor.authorPetruńko, Leon
dc.contributor.authorGmiter, Dawid
dc.date.accessioned2024-09-24T10:27:58Z
dc.date.available2024-09-24T10:27:58Z
dc.date.issued2024-09-18
dc.identifier.issn1730-2366
dc.identifier.urihttp://hdl.handle.net/11089/53225
dc.description.abstractThe Average Nucleotide Identity (ANI) was proposed as a standard for taxonomic affiliation of newly sequenced bacterial genomes. However, usage of ANI value as a means of strains phenotypic diversity offers a relatively easy way for studding bacterial phylogeny. Here we present a simple approach to bacterial genomes comparison based on ANI using fastANI and ANIclustermap. Both programs are available as an open-source tools and can be run using simple command lines. We present protocol for programs installation as a conda packages, that facilitate it utilization. Further, we explain how to prepare commands to perform the analysis. We believed our work could be useful for young scientist that begin their experience with bioinformatics.en
dc.language.isoen
dc.publisherWydawnictwo Uniwersytetu Łódzkiegopl
dc.relation.ispartofseriesActa Universitatis Lodziensis. Folia Biologica et Oecologicaen
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0
dc.subjectbacterial genomes comparisonen
dc.subjectbacterial phylogenyen
dc.subjectAverage Nucleotide Identity (ANI)en
dc.subjectfastANIen
dc.subjectANIclustermapen
dc.titleSimple approach to bacterial genomes comparison based on Average Nucleotide Identity (ANI) using fastANI and ANIclustermapen
dc.typeArticle
dc.page.number66-71
dc.contributor.authorAffiliationMusiał, Klaudia - Jan Kochanowski University of Kielce, Faculty of Natural Sciences, Institute of Biology, Department of Microbiology, Polanden
dc.contributor.authorAffiliationPetruńko, Leon - Jan Kochanowski University of Kielce, Faculty of Natural Sciences, Institute of Biology, Department of Microbiology, Polanden
dc.contributor.authorAffiliationGmiter, Dawid - Jan Kochanowski University of Kielce, Faculty of Natural Sciences, Institute of Biology, Department of Microbiology, Polanden
dc.identifier.eissn2083-8484
dc.referencesArahal, D.R. 2014. Whole-genome analyses: Average nucleotide identity. [In:] Methods in Microbiology, Vol. 41, pp. 103–122.en
dc.referencesBuermans, H.P.J., den Dunnen, J.T. 2014. Next generation sequencing technology: Advances and applications. Biochimica et Biophysica Acta – Molecular Basis of Disease, 1842(10), 1932–1941.en
dc.referencesDeurenberg, R H., Bathoorn, E., Chlebowicz, M.A., Couto, N., Ferdous, M., García-Cobos, S., Kooistra-Smid, A.M. D., Raangs, E.C., Rosema, S., Veloo, A.C. M., Zhou, K., Friedrich, A.W., Rossen, J.W.A. 2017. Application of next generation sequencing in clinical microbiology and infection prevention. Journal of Biotechnology, 243, 16–24.en
dc.referencesEdwards, D.J., Holt, K.E. 2013. Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data. Microbial Informatics and Experimentation, 3(1), 2.en
dc.referencesFigueras, M.J., Beaz-Hidalgo, R., Hossain, M.J., Liles, M.R. 2014. Taxonomic affiliation of new genomes should be verified using Average Nucleotide Identity and Multilocus Phylogenetic Analysis. Genome Announcements, 2(6), e00927-14-e00927-14.en
dc.referencesGmiter, D., Nawrot, S., Pacak, I., Zegadło, K., Kaca, W. 2021. Towards a better understanding of the bacterial pan-genome. Acta Universitatis Lodziensis. Folia Biologica et Oecologica, 17, 84–96.en
dc.referencesGoris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P., Tiedje, J.M. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. International Journal of Systematic and Evolutionary Microbiology, 57(1), 81–91.en
dc.referencesHodkinson, B.P., Grice, E.A. 2015. Next-Generation Sequencing: A Review of technologies and tools for wound microbiome research. Advances in Wound Care, 4(1), 50–58.en
dc.referencesJain, C., Rodriguez-R, L.M., Phillippy, A.M., Konstantinidis, K.T., Aluru, S. 2018. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature Communications, 9(1), 1–8.en
dc.referencesKobras, C.M., Fenton, A.K., Sheppard, S.K. 2021. Next-generation microbiology: from comparative genomics to gene function. In Genome Biology (Vol. 22, Issue 1). BioMed Central Ltd.en
dc.contributor.authorEmailMusiał, Klaudia - musial.klaudia0805@gmail.com
dc.contributor.authorEmailPetruńko, Leon - leonpetrunko@gmail.com
dc.contributor.authorEmailGmiter, Dawid - dawid.gmiter@ujk.edu.pl
dc.identifier.doi10.18778/1730-2366.18.10
dc.relation.volume18


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