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The Gibbs Motif Sampler specifications

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Unique identifier OMICS_00496
Name The Gibbs Motif Sampler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.1
Stability Stable
Maintained No

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Information


Unique identifier OMICS_00496
Name The Gibbs Motif Sampler
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.1
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Publications for The Gibbs Motif Sampler

library_books

The Gibbs Centroid Sampler.

2007 Nucleic Acids Res
PMCID: 1933196
PMID: 17483517
DOI: 10.1093/nar/gkm265

The Gibbs Motif Sampler in publications

 (23)
PMCID: 5919752
PMID: 29208650
DOI: 10.1534/g3.117.300138

[…] macs2 v2.1.0 (), and their outputs were integrated for downstream analyses (see details in the supplemental material). prediction of dna motifs at potential yrr1-binding sites was performed using the gibbs motif sampler in cisgenome with some manual adjustment. sequence logos of predicted motifs were generated using weblogo v3.4 (; ). the height of each nucleotide letter represented […]

PMCID: 4438489
PMID: 25990515
DOI: 10.1038/srep10444

[…] 10.3% and 7.1% of the known motifs in trnasfac. this leads to some ambiguities regarding whether motif 2 is a high-quality real motif or a sequence pattern mixed with high-level of noise reported by the gibbs motif sampler. in addition, the core sequence pattern gcgcacnyg of motif 2 shares some similarities with a segment (positions 9-17) of the new motif, suggesting that it might be a variant […]

PMCID: 4191424
PMID: 25249619
DOI: 10.1093/nar/gku860

[…] promoters had more than one binding peak for nme2. we found that 21 out of 22 promoters tested showed enrichment in chip-pcr (fdr of <5%, supplementary figure s2a; supplementary table s3). using the gibbs motif sampler () we found a guanine-rich 12-mer sequence motif present in > 80% of nme2 chip-chip peaks, which is largely consistent with earlier reports of nme2 as a purine-binding […]

PMCID: 4057619
PMID: 24932218
DOI: 10.1186/1754-6834-7-89

[…] we conducted a promoter dna-binding motif search using 500 bp sequences extracted from the upstream regions of all the genes encoding the down-regulated proteins in the ∆slr1037 mutant using the gibbs motif sampler software [,]. this analysis showed that the top conserved motif identified was a palindrome containing 10 total sites with the dna sequence “ggcgatcgcc” (figure ) [,]. […]

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

[…] that 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 […]


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The Gibbs Motif Sampler institution(s)
Center for Computational Molecular Biology and the Division of Applied Mathematics, Brown University, Providence, RI, USA

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