bz-rates: A Web Tool to Estimate Mutation Rates from Fluctuation Analysis

G3 : Genes - Genomes - Genetics
Alexandre Gillet-MarkowskaGilles Fischer

Abstract

Fluctuation analysis is the standard experimental method for measuring mutation rates in micro-organisms. The appearance of mutants is classically described by a Luria-Delbrück distribution composed of two parameters: the number of mutations per culture (m) and the differential growth rate between mutant and wild-type cells (b). A precise estimation of these two parameters is a prerequisite to the calculation of the mutation rate. Here, we developed bz-rates, a Web tool to calculate mutation rates that provides three useful advances over existing Web tools. First, it allows taking into account b, the differential growth rate between mutant and wild-type cells, in the estimation of m with the generating function. Second, bz-rates allows the user to take into account a deviation from the Luria-Delbrück distribution called z, the plating efficiency, in the estimation of m. Finally, the Web site provides a graphical visualization of the goodness-of-fit between the experimental data and the model. bz-rates is accessible at http://www.lcqb.upmc.fr/bzrates.

References

Jun 14, 2005·Mathematical Biosciences·Qi Zheng
Jun 24, 2006·Methods in Enzymology·Patricia L Foster
Nov 1, 1943·Genetics·S E Luria, M Delbrück
Jan 19, 2008·Genetics·Gregory I Lang, Andrew W Murray
Sep 30, 2008·Mathematical Biosciences·Qi Zheng
Dec 19, 2013·PloS One·Bernard Ycart
Dec 1, 1949·Journal of Genetics·D E LEA, C A COULSON
Jul 6, 2014·PloS One·Bernard Ycart, Nicolas Veziris

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Citations

Jun 3, 2020·Journal of Bacteriology·Rupal JainDennis W Grogan
Nov 1, 2017·G3 : Genes - Genomes - Genetics·Qi Zheng
Jan 18, 2018·Journal of Molecular Microbiology and Biotechnology·Eugene Y Wu, Angela K Hilliker
Apr 25, 2018·Nature Communications·Erik Wistrand-YuenDan I Andersson
May 23, 2019·Nucleic Acids Research·Emilia Puig LombardiArturo Londoño-Vallejo
Dec 7, 2019·Proceedings of the National Academy of Sciences of the United States of America·Alex RosenbergL David Sibley
Sep 25, 2020·Proceedings of the National Academy of Sciences of the United States of America·Sophie LoeilletAlain G Nicolas
Oct 16, 2020·PLoS Genetics·Danielle N GallagherJames E Haber
Mar 6, 2021·Nature Ecology & Evolution·Fernanda PinheiroMichael Lässig
Mar 22, 2021·Molecular Biology and Evolution·Kedar KarkareTim F Cooper
Apr 7, 2021·G3 : Genes - Genomes - Genetics·Corinne MaufraisGuilhem Janbon
May 22, 2021·Microbiology Resource Announcements·Qi Zheng
Jun 10, 2021·Nucleic Acids Research·Emil D JensenJay D Keasling
Jul 2, 2021·Nature Communications·Haoxuan Liu, Jianzhi Zhang
Sep 27, 2018·ACS Synthetic Biology·Anna J SimonAndrew D Ellington
Aug 25, 2021·Proceedings of the National Academy of Sciences of the United States of America·Juhyeon LimHyungjin Eoh

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Software Mentioned

rates
bz

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