PhysBinder protocols

View PhysBinder computational protocol

PhysBinder statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Transcription factor binding site prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

PhysBinder specifications

Information


Unique identifier OMICS_12907
Name PhysBinder
Interface Web user interface
Restrictions to use None
Input data Genomic sequences
Input format FASTA-formatted sequences
Output data Summary table
Programming languages Javascript, Perl, PHP
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Pieter De Bleser <>

Publication for PhysBinder

PhysBinder in pipeline

2017
PMCID: 5435695
PMID: 28515481
DOI: 10.1038/s41598-017-02291-1

[…] databases. logo representation of base conservation was obtained by the weblogo software., the prediction of sp1 binding sites in putative g4 forming sequences were performed by the web-based tool physbinder using the model hsa0000031.1 [sp1] with the max. f-measure threshold (2 × true positives/(2 × true positives + false positives + false negatives)., the evolutionary history was inferred […]


To access a full list of citations, you will need to upgrade to our premium service.

PhysBinder in publications

 (7)
PMCID: 5815073
PMID: 29309647
DOI: 10.1093/nar/gkx1242

[…] and calculation of position weight matrix from chip-seq peaksdna sequences of chip-seq peak regions for jund, c-jun and c-myc (for k562 and hela, for other tfs and cell lines ) were input data for physbinder to extract corresponding binding motifs. the ‘max. precision value (ppv)’ option was used for the analysis ().the resulting binding motifs were converted into pwms (position weight […]

PMCID: 5493129
PMID: 28680507
DOI: 10.1186/s13148-017-0367-x

[…] or molecular assay not specific to tissue source cregres coeff refers to the regression coefficient from beta regressions dtfb identified via motifmap etfb identified via encode ftfb identified via physbinder (avg precision) gtfb identified via hmr conservation 1smith et al. [] 2thaler et al. []; fuchikami et al. []; martinowich et al. []; dennis et al. [] 3weder et al. [] fig. 1 , note: […]

PMCID: 5473491
PMID: 28652783
DOI: 10.2147/AABC.S123604

[…] intronic, and 3′ utrs could be very helpful. common tfbs associated with diseased genes such as myc, jun, and zinc finger are searched for alternative targets with tfbs prediction tools such as physbinder, and experimental prediction tools such as qiagen’s chip qpcr search (http://www.sabiosciences.com/chipqpcrsearch.php) can be used as validation tool if the snps lie in those regions. […]

PMCID: 5435695
PMID: 28515481
DOI: 10.1038/s41598-017-02291-1

[…] sites for only a very few viruses are available in the literature, the establishment of a straightforward correlation between ltr g4s and sp1 was not possible. we thus used the online software physbinder to predict sp1 binding regions in the ltr of all lentiviruses with relevant pqss. in the primate lentiviruses, 30 out of 32 subgroups displayed sp1 binding sites that overlapped […]

PMCID: 5522290
PMID: 28465487
DOI: 10.18632/oncotarget.17118

[…] = 16; low imp3: n = 12)., mega 6 was used to represent the conservation of consensus sequence in imp3 binding sites at p65 3′utr. prediction of p65 binding sites on imp3 promoter was performed using physbinder (http://bioit.dmbr.ugent.be/physbinder/index.php) []., a computational approach of gsea [] was undertaken to evaluate the tcga agilent microarray data for the enrichment of genes […]


To access a full list of publications, you will need to upgrade to our premium service.

PhysBinder institution(s)
Department for Molecular Biomedical Research, VIB, Ghent University, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
PhysBinder funding source(s)
Agency for Innovation through Science and Technology in Flanders: [091213]; Research Foundation - Flanders (FWO): [G.0235.10].

PhysBinder reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PhysBinder