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GimmeMotifs specifications

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Unique identifier OMICS_02150
Name GimmeMotifs
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format BED, FASTA
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Simon J. van Heeringen <>

Publication for GimmeMotifs

GimmeMotifs in publications

 (13)
PMCID: 5899830
PMID: 29649445
DOI: 10.1016/j.chom.2018.03.007

[…] in promoter regions that are bound by specific tfs in a stage-specific manner. to identify dna motifs that could perform this function, we first performed an exhaustive de novo motif search using gimmemotifs and seqgl (; , ). these de novo predicted motifs were combined with previously predicted plasmodium motifs () and known vertebrate, invertebrate, and plant motifs from the cis-bp database […]

PMCID: 5662751
PMID: 29084942
DOI: 10.1038/s41467-017-01126-x

[…] finding programs: homer and dreme. we observed that all these analyses reported significantly enriched motifs with a core composed by ugu. thus, we performed motif clusterization with the program “gimmemotifs” (supplementary fig. ) and found two consensus motifs of 4 and 5-nt long, respectively (fig. ). each motif corresponds to many different words that belong to the motif with different […]

PMCID: 5343461
PMID: 28276452
DOI: 10.1038/srep43861

[…] to find their similarity based on a threshold e-value cut-off of 0.05 and minimum overlap of seven nucleotides. the motifs that were found to be similar were clustered using a python script from the gimmemotifs software to produce an average position weight matrix of all the similar motifs. again, using the tomtom tool, the clustered average matrix was queried against the motifs with known […]

PMCID: 5355061
PMID: 28030795
DOI: 10.18632/oncotarget.14150

[…] annotated either as promoter (-500 bp to the transcription start site), exon, intron or intergenic (everything else)., for motif analysis of aml1-eto, cbfb-myh11 and pml-rara binding sites, we used gimmemotifs []., pathway and gene ontology (biological process) enrichment analysis was performed using molecular signature database of gene set enrichment analysis (gsea; […]

PMCID: 5927328
PMID: 27863248
DOI: 10.1016/j.cell.2016.09.034

[…] (). only motifs with direct evidence of binding in the species of vertebrate were selected. within each motif family, as annotated by cis-bp, all motifs were clustered using 'gimme cluster' from the gimmemotifs package () with a threshold of 0.9999. the annotation of motifs is based on the annotation of human in the cis-bp database. motifs were used for scanning if the assigned tf is expressed […]

GimmeMotifs institution(s)
Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, HB Nijmegen, Netherlands
GimmeMotifs funding source(s)
NWO-ALW (Netherlands Organization for Scientific Research-Research Council for Earth and Life Sciences, grant number 864.03.002); National Institutes of Health (grant number R01HD054356) with grants to G.J.C.V.

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