|HOMER (Hypergeometric Optimization of Motif EnRichment) is
a suite of tools for Motif Discovery and ChIP-Seq analysis.
It is a collection of command line programs for unix-style
operating systems written in mostly perl and c++. Homer was
primarily written as a de
novo motif discovery algorithm that is well suited
for finding 8-12 bp motifs in large scale genomics data.
(recommended): 2+ Gb memory (4-8+ Gb), 10+ Gb Hard Drive
space (50+ Gb)
Software Requirements: Unix compatible OS (or cygwin),
perl, gcc, make, wget, ghostscript, weblogo, blat
Full Program Download
Use this file for downloading and updating the full
HOMER program and associated data. For sequencing
data, there are a bunch of annotation files, etc., for
each version of the genome, and this script helps manage
those files. If you don't want to deal with
configuring HOMER's next-gen sequencing functionality,
but want to try it for motif finding, see below.
: Download configureHomer.pl (right
click and select "save link as") and place in a directory
dedicated for HOMER (such as homer/).
Run the script by typing "perl configureHomer.pl" -
consult the links below for more information.
Additional software and configuration will be required the
first time you install HOMER (see Installation
Click for detailed
To upgrade, change your directory to where you installed
HOMER, and type:
- or -
perl configureHomer.pl -install homer (this is good for
forcing the software to reinstall - preferred if you
think there is something wrong)
If something appears to be wrong, redownload the
"configureHomer.pl" script and use "perl configureHomer.pl
-install homer" - this fixes a majority of issues.
Program Components and Older Versions
- Short description of recent changes
- Current HOMER
configuration list (Currently support human
hg17/hg18/hg19, mouse mm8/mm9, rat rn4, X. tropicalis
xenTro2, drosophila dm3, and C. elegans ce6, Zebrafish
danRer7, yeast sacCer2, Arabidopsis tair10, Rice msu6,