Motif Sampler statistics

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Motif Sampler specifications

Information


Unique identifier OMICS_06284
Name Motif Sampler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Gert Thijs <>

Information


Unique identifier OMICS_06284
Name Motif Sampler
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Gert Thijs <>

Publication for Motif Sampler

Motif Sampler in publications

 (7)
PMCID: 3855595
PMID: 24324603
DOI: 10.1371/journal.pone.0080511

[…] concentrate posterior mass: one with configurations such that and another with configurations further away, satisfying ., in this paper we have presented a bayesian approach, similar to the gibbs motif sampler in , , that jointly models motif and background compositions and binding site locations in a set of sequences. more importantly, we discuss and formalize an inferential procedure based […]

PMCID: 3509107
PMID: 23209563
DOI: 10.1371/journal.pone.0049086

[…] each of these loci is assume to hold a binding site with a certain probability. the algorithms operate on the sequences finding common motifs. examples of these techniques include alignace , gibbs motif sampler , meme , phylogibbs or weeder . we term them constrained algorithms since they are designed to find only one motif or a small set of motifs from an experiment. their outcome is cell […]

PMCID: 3820676
PMID: 24278755
DOI: 10.6064/2012/917540

[…] exactly one motif [] and the associated algorithm is called a site sampler. the second is more flexible and allows each sequence to have none or multiple motifs [] and the algorithm is termed a motif sampler. we will illustrate the site sampler and then briefly discuss the motif sampler. , i numerically illustrate the gibbs sampler algorithm for motif discovery. the main output of the gibbs […]

PMCID: 3603212
PMID: 22517426
DOI: 10.1093/bib/bbs016

[…] modify the current solution in a stochastic way. further improvements were introduced [] for allowing multiple occurrences (or no occurrence) of a motif within the same sequence (algorithm known as ‘motif sampler’). modifications of the basic gibbs sampling technique were also described for example in alignace [] and ann-spec []., the function used to assess profile significance […]

PMCID: 2566928
PMID: 18835840
DOI: 10.1093/pcp/pcn129

[…] methods have been used to find cis-regulatory elements in a given gene group in silico. multiple em for motif elicitation (meme; bailey and elkan , bailey et al. ), alignace (hughes et al. ) and motif-sampler (thijs et al. , thijs et al. ) are popular standards used in this field. these software packages utilize expectation maximization (em) or the gibbs sampling algorithm and can find […]


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Motif Sampler institution(s)
ESAT-SCD, KULeuven, Leuven, Belgium; Plant Genetics, VIB, University Gent, Gent, Belgium; INRA associated laboratory, VIB, University Gent, Gent, Belgium

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