# MousebreedeR: A novel software to assist in the design of breeding schema for complex genotypes of experimental organisms

## TL;DR

MousebreedeR is a software tool that helps researchers design breeding plans for mice with complex genetic traits.

## Contribution

It introduces a novel approach to optimize breeding schemes for multiple genetic loci in experimental organisms.

## Key findings

- MousebreedeR calculates breeding probabilities and provides efficient breeding strategies for multiple genetic loci.
- The tool includes visualization features to help researchers understand and plan crosses effectively.
- It is available as a free and open-source web app and R package.

## Abstract

With the advent of gene editing playing a regular role in producing new experimental models, the need to get the appropriate allele at each respective locus in a model organism is now common. Instead of simple “knockout” vs “wildtype” mouse experiments, for example, it is common for there to be a gene of interest that is either floxed (surrounded by known genetic sequence that allow for a gene to be knocked out when coexpression of the cre protein is expressed) or not floxed depending on the experimental group, another gene that marks cells of a certain phenotype such as a fluorescent reporter, a cre expression cassette to flox the gene of interest out, and more. While it is often obvious how to efficiently breed experimental organisms to obtain one locus of interest, once three or more loci are involved this becomes difficult to assess. MousebreedeR is a free and open source web-based shiny app and command line R package that takes desired mouse genotypes as well as the genotypes of potential mouse breeders that the user already has on hand as inputs, and delivers efficient breeding schema as the output. In addition, it supplies the user with the probability of producing each potential pup, the probability that no pups with the desired genotype are born in a litter, and more. We have also supplied code that assists the user in plotting these tables to help them visualize crosses of interest and make decisions in their breeding.