TOOLS | Judith Berman Lab

TOOL DEVELOPMENT

Software

Yeast Mapping Analysis Pipeline (YMAP)

An online webserver for the visualization of yeast genome sequence datasets that provides intuitive maps of aneuploidies and the degree of heterozygosity across all chromosomes.

YMAP detects copy number variations (CNVs) and loss of heterozygosity (LOH) events in eukaryotic genomes. It produces maps for lab strains with available haplotype maps and for clinical strains (in which a phylogeny is known). If a reference genome is uploaded, it can map chromosomes for additional yeast genomes.

See: Hickman, et al., 2016

diskImageR

A package for R which provides a quantitative, unbiased method to analyze photographs of disk diffusion assays for any microbial species/microbial drug combination.

The method measures the radius of inhibition ("RAD", i.e., resistance) at three different cutoff values (80%, 50% and 20% growth inhibition) as well as two measures of tolerance, the fraction of growth achieved above RAD ("FoG"), and drug sensitivity ("slope", the rate of change from no growth to full growth).

Available on:

See: Gerstein, et al., 2016

ColonyScanalyser

An image analysis tool for measuring microorganism colony growth. ColonyScanalyser will analyse and collate statistical data from agar plate images. It provides fast, high-throughput image processing.

ColonyScanalyser can provide information on colony appearance time, growth parameters (lag time, rate, carrying capacity), growth and appearance time distribution, and colony colour (e.g. staining or other visual indicator)

Available on:

See: ColonyScanalyser on GitHub

Transposon pipeline

A python package that uses machine learning to give genome-wide predictions of essential and non-essential genes for growth in yeast species under a given environmental condition.

The transposon pipeline uses an insertion mutant library generated from in vivo transposon experiments in a yeast species to identify genes important for growth, and infer essentiality of those genes. Training sets using gene essentiality data generated by classical genetic approaches for Saccharomyces cerevisiae and Schizosaccharomyces pombe are combined with this data to identify a core set of orthologs essential in all three yeasts.

Available on:

Transposon library available upon request.

Plasmids

Our lab has constructed a series of plasmids that enable tagging of genes at the N- or C- terminus with fluorescent proteins or epitope tags for protein analysis, described in Gerami-Nejad et al., Yeast 2001, 2004, and 2009.

Plasmids are available through The Fungal Genetics Stock Center (FGSC)