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HOMER (v4.2, 4-11-2012)

Software for motif discovery and next generation sequencing analysis

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 sets.

News

(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

(10-15-2012) 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.

Old News

Program Download

Download Page - Get the latest version of HOMER

Supported 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.

Using HOMER

Introduction to HOMER

Duff-sponsored Tutorials

Next-gen Sequencing Tutorial [PDF]

Helps guide and explain how to use HOMER for ChIP-Seq/GRO-Seq/MNase-Seq/DNase-Seq/RNA-Seq etc. analysis

New: A general introduction to next-gen sequencing analysis (useful if you are new to sequencing)

Old tutorial: Analysis of ChIP-Seq experiments using HOMER (some of this is out-of-date)

Motif Finding Tutorial [PDF]

Instructions and advice for finding enriched regulatory elements from a set of genome positions, a list of genes, or raw FASTA files.
Hi-C Analysis Tutorial [PDF]
Description of routines for analysis of Hi-C data to study genome conformation and structure.
Doughnut Documentation

Primary Data Download

UCSC Visualization files (Updated for errors in UCSC processing 08/31/10)

HOMER Known Motifs - Genome-wide predictions and UCSC Track

These tracks display motif positions genome-wide for human and mouse.  They are based on HOMER-motifs, and certainly miss many "weak" binding sites and incorrectly predict others.  However, the preictions can still serve as a useful guide to where factors are likely to bind (if they're expressed in the system you're studying).

Mouse mm9 UCSC BigBed Track (load as a custom track) - [primary BED file]
Human hg18 UCSC BigBed Track (load as a custom track) - [primary BED file]
Human hg19 UCSC BigBed Track (load as a custom track) - [primary BED file]

Data included in HOMER that may be useful for other purposes



Credits

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:
Heinz S, Benner C, Spann N, Bertolino E et al. 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

Link to the raw data: GSE21512
Can't figure something out? Questions, comments, concerns, or other feedback:
cbenner@ucsd.edu