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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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This tool is not available anymore.

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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 citations

 (23)
library_books

Transcriptional Profiling of Saccharomyces cerevisiae Reveals the Impact of Variation of a Single Transcription Factor on Differential Gene Expression in 4NQO, Fermentable, and Nonfermentable Carbon Sources

2017
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 […]

library_books

A novel DNA sequence motif in human and mouse genomes

2015
Sci Rep
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 […]

library_books

Non metastatic 2 (NME2) mediated suppression of lung cancer metastasis involves transcriptional regulation of key cell adhesion factor vinculin

2014
Nucleic Acids Res
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 […]

library_books

Butanol tolerance regulated by a two component response regulator Slr1037 in photosynthetic Synechocystis sp. PCC 6803

2014
Biotechnol Biofuels
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 ) [,]. […]

library_books

Bayesian Centroid Estimation for Motif Discovery

2013
PLoS One
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 […]

library_books

Genome wide distribution of histone H4 Lysine 16 acetylation sites and their relationship to gene expression

2013
PMCID: 3667149
PMID: 23587301
DOI: 10.1186/2041-9414-4-3

[…] and cell growth [,]. the h4k16ac associated dnas were also analyzed to determine whether a unique or novel dna motif was over-represented in the bound dnas. analysis of all 25,893 binding peaks with the gibbs motif sampler [] identified a 12-mer g-rich sequence motif (figure  c). this motif is present at least once in more than 55% of all h4k16ac peaks identified in hek293 cells. since […]


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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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