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

Installation

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 http://downloads.sourceforge.net/project/libpng/libpng16/older-releases/1.6.2/libpng-1.6.2.tar.gz

$ tar xvzf libpng-1.6.2.tar.gz

$ cd libpng-1.6.2/

$ ./configure --prefix=`pwd`

$ make

$ sudo make install

$ LIBPNGDIR=`pwd`

$ cd ../

Now, download and install BLAT.

$ wget http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip

$ unzip blatSrc35.zip

$ 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.

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Reference

1. Kent, W. J. (2002). BLAT—the BLAST-like alignment tool. Genome research, 12(4), 656-664.