|HOMER (Hypergeometric Optimization of Motif EnRichment) is
a suite of tools for Motif Discovery and next-gen sequencing
analysis. It is a collection of command line programs
for unix-style operating systems written in Perl and C++.
HOMER was primarily written as a de novo motif discovery algorithm and is
well suited for finding 8-20 bp motifs in large scale
genomics data. HOMER contains many useful tools for
analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and
numerous other types of functional genomics sequencing data
New version v4.3. Lots of new features including
scripts for processing files in batch. Bug fixes
(4-11-2013) New version v4.2, lots of updates and bug
fixes. Many of the genome versions and
annotations etc. have been updated (or are currently
being loaded on the website). Pombe & rice genomes
have been added. Arabidopsis has been
reconfigured to use Ensembl-style chromosome names
(i.e. "1" not "Chr1" as the last homer version
used. Sorry in advance!). Additional
documentation will be added soon...
(11-2-2012) New version v4.1, lots of bug fixes
New version v4.0! Full
integration of Hi-C analysis routines, updated annotation
files, plus minor bug fixes and updates. Lots of
updated documentation too.
Page - Get the latest version of HOMER
Organisms: Human (hg17, hg18, hg19),
Mouse (mm8, mm9, mm10), Rat (rn4, rn5), Frog
(xenTro2, xenTro3), Zebrafish (danRer7),
Drosophila (dm3), C elegans (ce6, ce10), S.
cerevisiae (sacCer2, sacCer3), pombe (ASM294v1),
Arabidopsis (tair10), Rice (msu6), and also works
with custom genomes in FASTA format and gene
annotations in GTF format.
Hi-C Analysis Tutorial [PDF]
Description of routines for analysis of Hi-C
data to study genome conformation and structure.
Primary Data Download
UCSC Visualization files (Updated for errors in UCSC
HOMER Known Motifs - Genome-wide predictions and UCSC
Data included in HOMER that may be useful for other
HOMER was developed
primarily by Chris Benner, with significant contributions
and suggestions by Sven Heinz, Kasey Hutt, Yin Lin, Gene
Hsiao, Fernando Alcalde, Josh Stender, Amy Sullivan,
Nathan Spann, Ivan Garcia-Bassets, Michael Lam, Michael
Rehli, and many others. Primary supervision for the
project was provided by Professors Christopher K. Glass
and Shankar Subramaniam.
Development of HOMER was carried out in the Glass
Lab at UCSD
For now, if you use HOMER in your research, please cite
the following paper:
Simple Combinations of
Lineage-Determining Transcription Factors Prime
cis-Regulatory Elements Required for Macrophage and B
Cell Identities. Mol Cell
2010 May 28;38(4):576-589. PMID: 20513432