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chevron_left Transcription factor binding site prediction De novo motif discovery Data integration chevron_right
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MotifLab specifications

Information


Unique identifier OMICS_00486
Name MotifLab
Software type Toolkit/Suite
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format FASTA, BED, GFF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 1.08
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Kjetil Klepper <>

Publication for MotifLab

MotifLab in pipelines

 (2)
2015
PMCID: 4514710
PMID: 26208222
DOI: 10.1371/journal.pone.0133280

[…] prediction tools such as wellington [], centipede [], dnase2tf [] and footprint detection software [] are available. we have devised an approach that uses dgf datasets from [], in combination with motiflab [] and four c-myb motifs from the transfac database [] and weighted conservation using mammalian phastcons elements []. our choice of conservation can be debated as regulatory elements may […]

2014
PMCID: 3928427
PMID: 24558479
DOI: 10.1371/journal.pone.0089110

[…] regions. further comparative analysis were yielded using r . proportional venn diagrams were plotted using made4 and venndiagram packages. chip-seq clustering was performed using diffbind tool ., motiflab tool was used to load ucsc tracks and evaluate region coverage of each criterion. peaks were then sorted according to these criteria. global mean rank varied according to the number […]


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MotifLab in publications

 (3)
PMCID: 4514710
PMID: 26208222
DOI: 10.1371/journal.pone.0133280

[…] where c-myb is upregulated: erythroleukaemia (k562) and promyelocytic leukaemia (nb4) []., to predict potential c-myb binding sites (c-myb footprints), we first scanned the human genome with motiflab [] using four c-myb motifs from the transfac database []. we identified more than 19 million c-myb motif instances and filtered these against cell-specific dnase i footprints from the six […]

PMCID: 4489807
PMID: 26134422
DOI: 10.1371/journal.pgen.1005337

[…] the chip binding regions, as most relevant cis elements have been reported to locate in that window [,]. we screened all the plant tf binding sites matrices from open-access libraries [–] with the motiflab software [], and found significant enrichment for the cis elements of 12 different tf families (), including bzip and indeterminate domain (idd) binding sites. interestingly, two recent […]

PMCID: 3928427
PMID: 24558479
DOI: 10.1371/journal.pone.0089110

[…] the structure of otx2 bound sequences, we searched nr and rpe core datasets for enriched motifs using three different tools: hypergeometric optimization of motif enrichment (homer), meme-chip and motiflab ( and and ). in the nr, all methods called the preferred otx2 binding site taatcc with flexible t/g sequence specificity at position 4. this motif was present in 67.2% of called peaks […]


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MotifLab institution(s)
Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway

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