DREME protocols

DREME specifications

Information


Unique identifier OMICS_06294
Name DREME
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline FIMO Team <>

Information


Unique identifier OMICS_06294
Name DREME
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline FIMO Team <>

Publication for DREME

DREME IN pipelines

 (4)
2016
PMCID: 5181583
PMID: 27803124
DOI: 10.1093/jxb/erw409

[…] upstream regions. the summits of overlapping peaks were used to define the location types in the genome as described previously (lu et al., 2013). motif enrichment analysis was performed by using dreme (bailey, 2011) with default parameters. sequences of 100 bp around the summits of overlapping peaks that appeared within 3-kb upstream regions were filtered by repeatmasker […]

2015
PMCID: 4683654
PMID: 26497144
DOI: 10.1534/g3.115.022517

[…] et al. 2015), it is feasible to search for regulatory elements within undefined promoter regions. we defined the promoter region as 1000 bp upstream of the transcriptional start site and used dreme (bailey 2011) to identify motifs overrepresented in the promoter regions of genes biased for expression in one sex and underrepresented in the promoter regions of genes biased for expression […]

2015
PMCID: 4701086
PMID: 26564160
DOI: 10.1534/genetics.115.182592

[…] al. 2013; figure 5a), although its rna-binding element is not yet known. to query for enrichment of 3′ utr motifs among its putative targets, we used the algorithms meme (bailey and elkan 1994) and dreme (bailey 2011), but found no enrichment for canonical cytoplasmic polyadenylation elements or other u-rich elements. to query for functional classes, we used david (huang et al. 2009a,b), […]

2013
PMCID: 3912905
PMID: 23895281
DOI: 10.1111/mmi.12345

[…] as the percentage of pcr product from the average of the immunoprecipitated samples normalized to the average of the input samples., motif prediction was carried out using the online version of dreme (bailey, 2011) using 100 bp sequences around the summits of the best peak for each intergenic region for all samples. shuffled input sequences were used for background comparison. significant […]

DREME institution(s)
Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia

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