Understanding the relationship between genes and proteins is crucial for elucidating biological processes, and disease mechanisms, and developing targeted therapies. A new tool developed by Yang et. al., [1], provides a better solution to map annotated positions and variants to protein structures automatically. 3Dmapper is a stand-alone tool based on R and Python programming languages that map annotated genomic variants or positions to protein structures [1]. In this article, we will install 3Dmapper on Ubuntu (Linux).
Preparing system
It is good to update and upgrade your Ubuntu system first. Log into your Ubuntu system and open the terminal by pressing Ctrl+Alt+T altogether, and type the following commands:
$ sudo apt-get update
$ sudo apt-get upgrade
Downloading Prerequisites
To run 3Dmapper, you need to have Python>3.6, R version > 3.5, BLAST, and GNU parallel. Paste the following commands to download them:
$ sudo apt-get install ncbi-blast+ r-base parallel
Installing 3Dmapper
Download the 3Dmapper using the following command:
$ git clone https://github.com/vicruiser/3Dmapper
Change to the new directory ‘3Dmapper‘.
$ cd 3Dmapper/
Now install it.
$ pip install .
$ sh r_dependencies.sh
It will take some time to finish the installation.
- Ruiz-Serra, V., Valentini, S., Madroñero, S., Valencia, A., & Porta-Pardo, E. (2024). 3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures. Bioinformatics, 40(4), btae171.
