Installing BLAT- A Pairwise Alignment Tool on Ubuntu

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Installing BLAT on Ubuntu

BLAT is a pairwise sequence alignment algorithm that is used in the assembly and annotation of the human genome [1]. In this article, we will install BLAT on Ubuntu.

Getting started

Let’s update and upgrade the system first.

$ sudo apt-get update

$ sudo apt-get upgrade


The first step in installing BLAT is to get libpng. Change to the directory where you want to install. In a terminal, type:

$ cd Downloads/

$ wget

$ tar xvzf libpng-1.6.2.tar.gz

$ cd libpng-1.6.2/

$ ./configure --prefix=`pwd`

$ make

$ sudo make install


$ cd ../

Now, download and install BLAT.

$ wget

$ unzip

$ cd blatSrc/

$ cp $LIBPNGDIR/png.h lib/

$ cp $LIBPNGDIR/pngconf.h lib/

$ cp $LIBPNGDIR/pnglibconf.h lib/

$ echo $MACHTYPE

It will display the OS and hardware. For example, ‘x86_64-ubuntu-linux-gnu’.

$ MACHTYPE=x86_64

$ export MACHTYPE

$ mkdir -p ~/bin/$MACHTYPE

$ make

Export the path as shown below.

$ echo 'export MACHTYPE=x86_64' >> ~/.bashrc

$ echo 'export PATH=$PATH:~/bin/$MACHTYPE' >> ~/.bashrc

$ source ~/.bashrc

Now, you can easily run BLAT from the terminal. Type blatto run.


  1. Kent, W. J. (2002). BLAT—the BLAST-like alignment tool. Genome research12(4), 656-664.

Tariq is founder of Bioinformatics Review and a professional Software Developer 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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