Installing FragGeneScan on Ubuntu

FragGeneScan is a bioinformatics software to find fragmented genes in short reads [1]. It predicts genes by combining sequence models and codon usages in a hidden Markov model (HMM). It improves the prediction of the protein-coding region in short reads. In this article, we will install FragGeneScan on Ubuntu.

Getting started

Let’s update and upgrade the system first.

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading

To download, FragGeneScan, open a terminal (Ctrl+Alt+T) and change to the directory where you want to download the software. Let’s say Downloads and type the following command on the terminal:

$ cd Downloads/

$ wget https://sourceforge.net/projects/fraggenescan/files/latest/download/FragGeneScan1.31.tar.gz

If you want to download it manually, then click here.

Installation

Now, type the following commands from the same directory:

$ tar xvzf FragGeneScan1.31.tar.gz

$ cd FragGeneScan1.31/

$ make

$ make clean

$ make fgs

Now, you can easily run FragGeneScan from the terminal.

References

1. Rho, M., Tang, H., & Ye, Y. (2010). FragGeneScan: predicting genes in short and error-prone reads. Nucleic acids research, 38(20), e191-e191.