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Number of citations per year for the bioinformatics software tool The Gibbs Motif Sampler
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Protocols

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.

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 citations

 (10)
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

[…] and 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 the poster […]

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 of […]

library_books

Bayesian Centroid Estimation for Motif Discovery

2013
PLoS One
PMCID: 3855595
PMID: 24324603
DOI: 10.1371/journal.pone.0080511

[…] 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 procedu […]

call_split

Study of PcaV from Streptomyces coelicolor yields new insights into ligand responsive MarR family transcription factors

2013
Nucleic Acids Res
PMCID: 3616709
PMID: 23396446
DOI: 10.1093/nar/gkt009
call_split See protocol

[…] Regulatory motifs were predicted using the Gibbs Motif Sampler (). The Gibbs recursive sampler with prokaryotic default settings was used. Intergenic sequences between the pcaV gene and pcaI/pcaH genes in various Streptomyces species were […]

library_books

Efficient Identification of Transcription Factor Binding Sites with a Graph Theoretic Approach

2013
PMCID: 3549379
PMID: 23365625
DOI: 10.1155/2013/856281

[…] predict the binding sites for two organisms, Caenorhabditis elegans and mus musculus. We evaluated the prediction accuracy of our approach based on the testing data sets and compared it with that of the Gibbs Motif Sampler []. Our testing results showed that our approach can achieve an average developer score of 0.90 on the test data, which is higher than or comparable with that of the Gibbs Samp […]

call_split

RNA seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803

2012
Biotechnol Biofuels
PMCID: 3564720
PMID: 23259593
DOI: 10.1186/1754-6834-5-89
call_split See protocol

[…] The Gibbs Motif Sampler software from the Biometrics Laboratory of Wadsworth Center, ( http://www.bayesweb.wadsworth.org/gibbs/gibbs.html), was used to identify matrix models describing DNA sequence m […]


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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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