DREME protocols

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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

 (18)
2017
PMCID: 5282726
PMID: 28137275
DOI: 10.1186/s13059-017-1150-1

[…] file : table s3 for a summary of the mapping step. peaks of read enrichment were detected using macs [] version 2.1.0.20140616. further analyses were performed by means of bedtools [], deeptools [], dreme [], and custom bash, r, and python scripts., additional file 1: , the genomic dna sample for leishmania donovani gr383wt1 was provided courtesy of prof. charles l. jaffe (national center […]

2017
PMCID: 5340393
PMID: 28267806
DOI: 10.1371/journal.pone.0173421

[…] replicates were defined as high-confidence peaks and used for further analysis. the 101 nucleotides centered on the summits detected by macs2 were used for detection of the consensus m6a motif by dreme (version: 4.10.2) []. motif central enrichment was performed by centrimo (version: 4.10.2) [] with 301 nucleotides centered on the summits. to compare the positional distribution of the motif […]

2017
PMCID: 5429541
PMID: 28507606
DOI: 10.1186/s13072-017-0133-5

[…] dna methylation, rna-seq and chip-seq data were analysed using seqmonk v0.29.0–0.34.0. pc analysis and statistical analyses were performed in r v.3.0.2. motif enrichment analysis was performed using dreme [] and meme [] within the meme suite v4.11.1 with default parameters specifying list of control sequences. enriched motifs were directly submitted to tomtom [] within the meme suite using […]

2017
PMCID: 5568443
PMID: 28800584
DOI: 10.1371/journal.ppat.1006560

[…] versions of those in tritrypdb (http://tritrypdb.org/tritrypdb/), and categories were assigned manually. other statistical analysis was done in r. the 3’ utr motif enrichment search was done using dreme []; annotated 3’-utr sequences were downloaded from tritrypdb and we considered only the mrnas with 3’ utrs >20 nt. manual 3'-utr annotation was done using the rnaseq reads and poly(a) site […]

2017
PMCID: 5735166
PMID: 29255196
DOI: 10.1038/s41467-017-02150-7

[…] sequences of vanc21-enriched regions defined by macs2 in vandal21 tes were extracted. short motifs that were statistically enriched at the vanc21-binding regions in vandal21 tes were searched by a dreme script of meme software (4.11.0) under default parameters except maximum core width was set as 9. same parameters were used for searching short motifs at cg-dmrs induced by vanc genes […]


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DREME in publications

 (160)
PMCID: 5935921
PMID: 29728068
DOI: 10.1186/s12864-018-4691-0

[…] in previous study []. for motif analysis, tools of meme suite (v.4.12.0) were used with default settings []. motif discovery was performed with discriminative regular expression motif elicitation (dreme) with entire homoeologous gene promoters and extracted subgenome independent promoters. to evaluate the biased distribution, analysis of motif enrichment (ame) was used. functional annotation […]

PMCID: 5908872
PMID: 29674676
DOI: 10.1038/s41598-018-23207-7

[…] to transform the count data to the log2 scale; this transformation minimizes differences between samples for genes with small counts and normalizes the counts with respect to library size., we used dreme in conjunction with tomtom and jaspar to identify putative transcription factor binding sites (tfbfs) in gene promoters. gene promoters were defined as 1000-bp-long sequences starting 750 bp […]

PMCID: 5894230
PMID: 29636001
DOI: 10.1186/s12870-018-1275-8

[…] transcription factor, the chip peak sequences were subjected to meme (multiple em for motif elicitation)-chip []. the meme-chip program uses two ab initio motif discovery algorithms: meme [], and dreme (discriminative regular expression motif elicitation) [], which uses regular expressions to search for short eukaryotic tf motifs that are missed by meme., in order to determine putative […]

PMCID: 5879934
PMID: 29609617
DOI: 10.1186/s13072-018-0183-3

[…] that this protein tends to associate with 5’utr and promoter regions of the genes that are specifically activated in testis (binomial test, p < 0.001, fig. b, additional file : fig. 10). using dreme platform, we found that cg9879-bound regions frequently contained at-rich motifs resembling the tata-box sequence (additional file : fig. 11) []. in general, cg9879 tends to co-localize […]

PMCID: 5877393
PMID: 29598823
DOI: 10.1186/s13059-018-1418-0

[…] for each unique pas significantly coupled to tsss or exons and for each unique pas that did not show a significant coupling., for pass that could not be attributed to known poly(a) signals, we ran dreme [] (v. 4.11.4) to identify enriched motifs. a randomly shuffled set of sequences was generated from the original sequences of the examined pass and used as a background set. in addition, […]


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

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