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Mutation Prediction

Installing SIFT for Missense Variants on Ubuntu

Tariq Abdullah

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installing SIFT on ubuntu

SIFT is a bioinformatics tool for predicting missense effects of non-synonymous/missense variations in sequences [1]. SIFT identifies naturally occurring nonsynonymous polymorphisms as well as laboratory-induced missense mutations. In this article, we will install SIFT 6.2.1 for missense variants prediction on Ubuntu.

Getting started

Let’s update and upgrade the system first.

Open the terminal (Ctrl+T) and type the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading SIFT 6.2.1

Change to the directory where you wish to download the software. You can either download it from here or use the following command:

$ cd Downloads/

$ wget https://s3.amazonaws.com/sift-public/nsSNV/sift6.2.1.tar.gz

Installing SIFT

Extract the archived file and then install it.

$ tar xvzf sift6.2.1.tar.gz

Change to the sift directory.

$ cd sift6.2.1/

Move inside the blimps directory present in sift and make.

$ cd blimps/

$ make clean

$ make all

$ cd ../

Now move inside the src directory and compile.

$ cd src/

$ ./compile.csh

It could take some time to finish depending upon your system configuration. That finishes your installation.


References

  1. Vaser, R., Adusumalli, S., Leng, S. N., Sikic, M., & Ng, P. C. (2016). SIFT missense predictions for genomes. Nature protocols11(1), 1.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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