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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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