Genomic intervals · Software
HOMER
Discovers sequence motifs and analyses functional genomics sequencing data such as ChIP-seq and RNA-seq.
What HOMER is
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of command-line tools designed for motif discovery and the analysis of next-generation sequencing experiments. Developed primarily by Chris Benner in the Benner Lab at UCSD, alongside previous work at the Salk Institute and the Glass Lab, it supports functional genomics data across multiple model organisms.
The software is designed to identify regulatory elements within large genomic datasets. It provides utilities for de novo motif discovery and handles specialised analysis pipelines for diverse experimental methodologies, including ChIP-seq, GRO-seq, RNA-seq, DNase-seq, MNase-seq, csRNA-seq, and Hi-C.
How it works
HOMER operates as a suite of tools written predominantly in Perl and C++ for UNIX-style systems. It identifies enriched regulatory motifs de novo using genomic coordinates, gene lists, or FASTA sequence inputs. The software also provides algorithms for positional sequence analysis, background sequence selection and modelling, and sequence variant analysis.
Beyond motif identification, HOMER annotates peaks and coordinates from sequencing experiments and provides genome-wide motif prediction tracks. While capable of analysing generic FASTA and GTF files, it integrates pre-compiled annotation support for several specific genome assemblies.
Key facts
- Full name
- Hypergeometric Optimization of Motif EnRichment
- Primary developer
- Chris Benner (Benner Lab, UCSD)
- Implementation languages
- Perl and C++
- Operating systems
- UNIX-style operating systems
- Target motif length
- 8 to 20 base pairs
- Supported assay types
- ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, MNase-Seq, csRNA-Seq, Hi-C
- Supported file formats
- FASTA, GTF, BigBed, BED, .motif
What you can use it for
- De novo motif discovery
- Detecting enriched sequence motifs between 8 and 20 base pairs in genomic regions, gene lists, or FASTA files.
- ChIP-seq peak annotation
- Annotating genomic intervals and identifying putative transcription factor binding sites across target regions.
- Nascent transcription analysis
- Analysing transcription start sites using csRNA-seq and GRO-seq sequencing datasets.
- Chromatin conformation analysis
- Processing and interpreting interaction datasets derived from Hi-C sequencing experiments.
Run it here
HOMER is preinstalled on the machine behind every research conversation. Ask the agent in plain language, or give it the exact command — it runs it, reads the output and explains it.
Strengths and limits
Good at
- Well suited for discovering de novo motifs between 8 and 20 base pairs in large-scale genomic datasets.
- Supports analysis workflows across a wide range of functional genomics assays, including ChIP-seq, csRNA-seq, and Hi-C.
- Offers built-in annotation resources for numerous model organisms, including human, mouse, rat, zebrafish, fruit fly, and yeast.
Watch out for
- Genome-wide motif predictions may omit weaker transcription factor binding sites while predicting false-positive sites.
- Certain analysis features rely on external third-party software such as R or samtools.
Questions
Can I run HOMER online without installing it?
HOMER is preinstalled on the machine behind every research conversation. Ask the agent in plain language, or give it the exact command — it runs it, reads the output and explains it.
What licence is HOMER under?
HOMER is published under its authors' own licence; the project page at http://homer.ucsd.edu/homer/ states it.
Which organisms have dedicated annotation support in HOMER?
HOMER includes specific annotation support for human, mouse, rat, frog, zebrafish, Drosophila, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis, and rice, though general tools accept any FASTA or GTF file.
What size of motifs is HOMER designed to identify?
HOMER was primarily written to identify de novo motifs between 8 and 20 base pairs in length.
Can HOMER analyse data from assays other than ChIP-seq?
Yes, the suite provides routines for GRO-seq, RNA-seq, DNase-seq, MNase-seq, csRNA-seq, and Hi-C functional genomics experiments.
How to cite it
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
Written from HOMER's own README and project page. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.