248    ◾    Bioinformatics

HOMER is another motif discovery program that has an algorithm which performs de

novo motif discovery in the regulatory regions of genes using a primary dataset and a sec-

ondary dataset. HOMER has two programs, findMotifs.pl and findMotifsGenome.pl, that

perform the motif discovery in promoter and genomic regions, respectively. However, for

ChIP-Seq enrichment sequences, we will use findMotifs.pl or homer2. Like MEME Suite

programs, HOMER can also create a secondary random dataset if you do not have one.

For the instructions of HOMER installation, visit “http://homer.ucsd.edu/homer/intro-

duction/install.html”. Homer includes a collection of perl and c++ programs designed to

run in a UNIX/Linux environment. Refer to the website for the program requirements.

On Ubuntu, after making sure that all required programs have been installed, you can

create a directory “homer”, download the installation Perl script, and install the HOMER

as follows:

mkdir homer; cd homer

wget http://homer.ucsd.edu/homer/configureHomer.pl

perl configureHomer.pl -install

After the installation is complete, you will get a message as follows:

Add this line to your .bash_profile or .bashrc file (or other depending on your shell):

PATH=$PATH:/home/username/downloads/homer/.//bin/

The path will depend on where you have installed HOMER. Copy the path and add it to the

end of “.bashrc” file as follows:

export PATH=$PATH:/home/username/downloads/homer/.//bin/:$PATH

You may need to restart the terminal or use “source ~/.bashrc” for the change to take effect.

To test HOMER installation, run “findMotifs.pl”. That will display HOMER usage and

option. The “findMotifs.pl” command requires your target sequences’ file and a background

sequence file in FASTA format specified by “-fasta” option. However, if you do not provide

a background sequences’ file, the command will use your target sequences to create back-

ground sequences. The general syntax for the use of “findMotifs.pl” command is as follows:

findMotifs.pl <targetSequences.fa> fasta <output directory> -fasta

<background.fa> [options]

We can use this command without providing background sequences’ file as follows:

findMotifs.pl chip1_peaks.fasta fasta homer_motifs_chip1/

findMotifs.pl chip2_peaks.fasta fasta homer_motifs_chip2/

findMotifs.pl chip3_peaks.fasta fasta homer_motifs_chip3/

Three output directories will be created and several files are produced in each of the output

directories: