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HOMER Plants

Software for motif discovery and ChIP-Seq analysis

Plant Genomes and Annotations

To help facilitate genomics research using plant model organisms, HOMER has been expanded to include annotation and genome information for several plant species. In addition to Arabidopsis, several other model crops, mosses, and algae have been added to HOMER's annotation packages.  HOMER can also be extended/customized to analyze additional organisms. 

Currently available organisms (genomes):

Most of the plant genomes were based on current EnsemblPlant annotations:

arabidopsis (Arabidopsis thaliana): tair10 (source)
corn (Zea mays): corn.AGPv3 (source)
rice (Oryza sativa): rice.IRGSP-1.0 (source)
patens (Physcomitrella patens): patens.ASM242v1 (source)
chlamy (Chlamydomonas reinhardtii): chlamy.v3.1 (source)

Adding new species to HOMER:

HOMER maintains annotation and sequence information for several different organisms that can be managed through the "configureHomer.pl" installation script.  However, HOMER can also be used with other organisms. Generally, there are two ways to use HOMER to analyze data with custom organisms/annotation. First, you may want to configure the organism yourself using loadGenome.pl script (more information available here Part [3]). Alternatively, many of HOMER's commands will work directly on FASTA or GTF/GFF files (see Part [2] for 'on-the-fly' analysis).

Nascent transcriptions from Arabidopsis:

Jonathan Hetzel and Sascha Duttke from the Chory Lab at Salk recently performed one of the first GRO-seq (Nascent RNA from global run-on sequencing) experiments in Plants. GRO-seq allows for the identification of transcripts independent of RNA stability, revealing unstable transcripts and pausing sites for RNA polymerase throughout the genome.  5'GRO-seq was also performed to map transcription initiation sites for all transcripts.
Transcript File

GRO-seq data for Arabidopsis: GSE83108

DAP-seq Motif Library:

Ronan O'Malley and colleagues in the Ecker lab at Salk recently developed an in vitro technique to rapidly profile putative transcription factor binding sites using a method called DAP-seq (link to the paper). Peaks identified in the paper were realized using HOMER to create a library of nearly 500 motifs that are available as part of HOMER.  Individual motif files for each experiment can be found in the motifs/plants/ directory where HOMER is installed.
Combined Motif File: arab.dap.motifs

Full Motif Library with Sequence Logos

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