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HOMER(v4.9, 2-20-2017)

Software for motif discovery and next generation sequencing analysis



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.

Hardware Requirements (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

Download file:

configureHomer.pl v4.9 (2-20-2017) [GPLv3]

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.

Instructions
: 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 installation instructions

To upgrade, change your directory to where you installed HOMER, and type:

perl configureHomer.pl -update
- 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

homer2 program - key exectuable for HOMER motif discovery (homerCppOnly.*.zip). (This archive actually contains all of the c++ exectuables, not just homer2).  Unzip in the desired directory and simply type "make" to compile the program.

The configuration script really doesn't deal with older versions, but you can download older versions yourself should you really feel like using inferior data or software!
Old Versions of HOMER Software
Old Versions of Organism Packages
Old Versions of Promoter Packages
Old Versions of Genome Packages

Update Information

Change Log - Short description of recent changes

update.txt - 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, Pombe ASM294v1)



Can't figure something out? Questions, comments, concerns, or other feedback:
cbenner@ucsd.edu