fur: Find Unique Regions

Description

The program fur takes as input a set of target genome sequences and a set of related genome sequences, the neighbors. It returns the sequence regions common to all targets that are absent form the neighbors. Such regions can be used as candidate genetic markers.

Authors

Bernhard Haubold and Beatriz Vieira Mourato

Make the Programs

If you are on an Ubuntu system like Ubuntu on wsl under MS-Windows or the Ubuntu Docker container, you can clone the repository and change into it.

git clone https://github.com/evolbioinf/fur
cd fur

Then install the additional dependencies by running the script setup.sh.

bash scripts/setup.sh

Make the programs.

make

The directory bin now contains the binaries.

Docker Container

As an alternative to building fur, we also post it as a docker container. The container includes all programs needed to work through the tutorial at the end of the documentation in ~/furDoc.pdf.

docker pull haubold/fox
docker run -it --detach-keys="ctrl-@" fox

License

GNU General Public License

References

Haubold, B., Klötzl, F., Hellberg, L., Thompson, D., & Cavalar, M. (2021). Fur: Find unique genomic regions for diagnostic PCR. Bioinformatics, 37(15), 2081-2087.

Vieira Mourato, B., Tsers, I., Denker, S., Klötzl, F., & Haubold, B. (2024). Marker discovery in the large. Bioinformatics Advances, 4(1), vbae113.