MotifViz protocols

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MotifViz statistics

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MotifViz specifications

Information


Unique identifier OMICS_08359
Name MotifViz
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Publication for MotifViz

MotifViz in pipeline

2011
PMCID: 3020958
PMID: 21249144
DOI: 10.1371/journal.pone.0016171

[…] platinum taq pcr reaction for 32 cycles. pcr products were separated on a 10% tbe gel (ready gel, biorad) and stained by sybr gold., nf-κb sites for study were selected by the clover algorithm of motifviz (http://biowulf.bu.edu/motifviz/), which uses the jaspar database (http://jaspar.genereg.net/) for its binding matrices. we selected κb sites for chip that had the best score for matching […]


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MotifViz in publications

 (6)
PMCID: 5363547
PMID: 27732936
DOI: 10.18632/oncotarget.12525

[…] the manufacturer's instructions. cell sorting was performed with a facsaria iii sorter (bd biosciences)., computational search for ets binding sites on selected gene promoters was performed using motifviz (biowulf.bu.edu/motifviz). chromatin immunoprecipitation was performed with anti-ese3 (clone 5a5.5, lab vision, fremont, ca usa); anti ach3 (upstate, millipore); anti h3k9 2met (upstate, […]

PMCID: 3060696
PMID: 21239383
DOI: 10.1093/jxb/erq416

[…] jxb online)., based on earlier studies of phenylpropanoid biosynthesis pathway-specific cis-elements (; ; ), 1000 bp upstream promoter regions of candidate abc transporter genes were examined using ‘motifviz’ (http://biowulf.bu.edu/motifviz). upstream promoter region sequences were obtained from the ‘the arabidopsis information resource’ (tair) database (http://arabidopsis.org) and analysed […]

PMCID: 3020958
PMID: 21249144
DOI: 10.1371/journal.pone.0016171

[…] platinum taq pcr reaction for 32 cycles. pcr products were separated on a 10% tbe gel (ready gel, biorad) and stained by sybr gold., nf-κb sites for study were selected by the clover algorithm of motifviz (http://biowulf.bu.edu/motifviz/), which uses the jaspar database (http://jaspar.genereg.net/) for its binding matrices. we selected κb sites for chip that had the best score for matching […]

PMCID: 2950082
PMID: 20706209
DOI: 10.1038/msb.2010.54

[…] genes was calculated using fisher's exact test executed in r and, when possible, ease ()., to identify sequence motifs that were overrepresented in the data, we used possum (http://biowulf.bu.edu/motifviz/) to generate log-likelihood scores for position weight matrices (pwms) (transfac 12.1). within 0–2 kb upstream of genes, we defined scores above 8 as matches to a pwm. pwms were defined […]

PMCID: 2758837
PMID: 19758441
DOI: 10.1186/1752-0509-3-93

[…] expression profiles from cyclebase.org [], candidate binding sites from jaspar [], and upstream sequences from genedb []. the dna motifs were searched against jaspar with stamp [] and plotted with motifviz []. the rna motifs were identified with fire and rnapromo [,]. sample skew and sample excess kurtosis of time courses were computed with the r package fints. the skew was computed […]


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MotifViz institution(s)
Bioinformatics Program and Biomedical Engineering Department, Boston University, Boston, MA, USA

MotifViz review

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