BLAT is a pairwise sequence alignment algorithm that is used in the assembly and annotation of the human genome . In this article, we will install BLAT on Ubuntu.
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 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`
$ sudo make install
$ 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’.
$ export MACHTYPE
$ mkdir -p ~/bin/$MACHTYPE
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
- Kent, W. J. (2002). BLAT—the BLAST-like alignment tool. Genome research, 12(4), 656-664.
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