accuMUlate: a mutation caller designed for mutation accumulation experiments

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accuMUlate: A mutation caller designed for mutation accumulation experiments.

Summary Mutation accumulation (MA) is the most widely used method for directly studying the effects of mutation. By sequencing whole genomes from MA lines, researchers can directly study the rate and molecular spectra of spontaneous mutations and use these results to understand how mutation contributes to biological processes. At present there is no software designed specifically for identifyin...

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Asymmetric Context-Dependent Mutation Patterns Revealed through Mutation-Accumulation Experiments.

Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5,645 spontaneous mutations in wild- type (WT) and mismatch-repair deficient (MMR(-)) mutation-accumulation (MA) lines of the gram-positive model organism Bacillus subt...

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DNA Sequence Fragment Containing C to A Mutation as a Convenient Mutation Standard for DHPLC Analysis

Objective(s):  Denaturing high performance liquid chromatography (DHPLC) is a high throughput approach for screening DNA sequence variations. To assess oven calibration, cartridge performance, buffer composition and stability, the WAVE Low and High Range Mutation Standards are employed to ensure reproducibility and accuracy of the chromatographic analysis. The purpose of this study was to provi...

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Comparing analysis methods for mutation-accumulation data.

THE genomic deleterious mutation rate (U) and the different algorithms to locate maxima (or minima) in the multidimensional parameter space. ML employs nudistribution of mutational effects for fitness, f(s), merical integration to compute likelihood of data as a are important parameters for several theoretical issues function of U and f(s) and combines grid searches with in evolution (Charleswo...

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 2018

ISSN: 1367-4803,1460-2059

DOI: 10.1093/bioinformatics/bty165