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MotifSuite specifications

Information


Unique identifier OMICS_09254
Name MotifSuite
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Kathleen Marchal <>

Information


Unique identifier OMICS_09254
Name MotifSuite
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Kathleen Marchal <>

Publication for MotifSuite

MotifSuite in pipeline

2017
PMCID: 5714201
PMID: 28977425
DOI: 10.1093/nar/gkx747

[…] jaspar core database (). peak sequences (input sequence) were scanned using the motiflocator software (). the second-order custom background model was created by createbackgroundmodel software in motifsuite using all peak sequences (). to assess the statistical significance of motiflocator scores, we randomized the input sequence and applied motiflocator to the randomized sequence using […]


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MotifSuite in publications

 (5)
PMCID: 5714201
PMID: 28977425
DOI: 10.1093/nar/gkx747

[…] jaspar core database (). peak sequences (input sequence) were scanned using the motiflocator software (). the second-order custom background model was created by createbackgroundmodel software in motifsuite using all peak sequences (). to assess the statistical significance of motiflocator scores, we randomized the input sequence and applied motiflocator to the randomized sequence using […]

PMCID: 4824487
PMID: 27055116
DOI: 10.1371/journal.pgen.1005893

[…] located in the middle were retrieved from hg19. two sequences with reference or alternative allele were generated for each candidate snp. the pwms were constructed based on the hocomoco database []. motifsuite was used to detect motifs within the query sequences showing better fits to the hocomoco pwms over the background model for human genome []., chip-seq data in hela-s3 cells were downloaded […]

PMCID: 4654594
PMID: 26587879
DOI: 10.1371/journal.pbio.1002307

[…] between motifs, we used position frequency matrices from the six positions downstream of ugua as input to motifcomparison (p-blic, 100 shuffles, no shift permitted between matrices) in the motifsuite []. motifcomparison calculated the p-value of the bayesian likelihood 2-component (blic) score [], and we considered two motifs to be similar if p < 0.05., motifs are displayed […]

PMCID: 4284222
PMID: 25559185
DOI: 10.1083/jcb.201405110

[…] on known yy1 responsive elements surrounding the surf1/2 gene (surfeit locus protein 1 and 2) and the emu enhancer from the igh locus size matched to fragment i, for comparison (fig. s4 d; ). using motifsuite, we estimate an approximately twofold enrichment of yy1 binding sites at lad borders (±10 kb) relative to chromosomal background (unpublished data; ). finally, the statistical correlation […]

PMCID: 3247239
PMID: 22085861
DOI: 10.1186/1471-2164-12-561

[…] whether reported motifs are truly enriched., for motifsampler [], we first created a second-order background model from our set of 2kb promoter regions using the createbackgroundmodel algorithm from motifsuite []. we then ran motifsampler using this background distribution and the -n 4 parameter (so that the best four motifs would be found). by default, motifsampler performs its analysis 100 […]


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MotifSuite institution(s)
Department of Microbial and Molecular Systems, Katholieke Universiteit Leuven, Kasteelpark Arenberg, Germany; Department of Electrical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg, Heverlee, Belgium; School of Life Sciences—LifeNet, Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany; Department of Plant Biotechnology and Bioinformatics (VIB), Ghent University, Technologiepark, Ghent, Belgium
MotifSuite funding source(s)
KU Leuven funding: (GOA/08/011, CoE EF/05/007); Agentschap voor Innovatie door Wetenschap en Technologie (IWT): (SBO-BioFrame); Interuniversity Attraction Poles (IAP) (P6/25); Fonds Wetenschappelijk Onderzoek-Vlaanderen (FWO): (IOK-B9725-G.0329.09, 5); Ghent University: (Multidisciplinary Research Partnership ‘M2N’)

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