Installing FragGeneScan on Ubuntu

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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


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

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


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.


  1. Rho, M., Tang, H., & Ye, Y. (2010). FragGeneScan: predicting genes in short and error-prone reads. Nucleic acids research38(20), e191-e191.
Muniba is a Bioinformatician based in the South China University of Technology. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

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