Virtual Footprint protocols

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Virtual Footprint specifications

Information


Unique identifier OMICS_26500
Name Virtual Footprint
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Maintainers


  • person_outline Dieter Jahn <>
  • person_outline Richard Munch <>

Additional information


http://www.prodoric2.de/vfprint.php

Publication for Virtual Footprint

Virtual Footprint in pipeline

2011
PMCID: 3177180
PMID: 21690099
DOI: 10.1093/nar/gkr338

[…] in aracne with a dpi of 0.1 (). the resulting networks were visualized using the cytoscape software application ()., to identify potential binding sites for ompr, we have used the online tool virtual footprint (http://prodoric.tu-bs.de/vfp/) using the prodoric library and performing the regulon and the promoter analysis (). the pwm (position weight matrix) considered were ompc-box […]


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Virtual Footprint in publications

 (18)
PMCID: 5459824
PMID: 28584275
DOI: 10.1038/s41598-017-03012-4

[…] of the major pathway in which each deg participated. gene promoters (for each gene, the sequence from position −350 bp to −1 bp was selected for analysis) and corresponding tfs were predicted by the virtual footprint program, v. 3.0. a proposed regulatory network of degs was generated using the cytoscape 3 software program., , qing wang and xu wang contributed equally to this work., […]

PMCID: 5398030
PMID: 28473807
DOI: 10.3389/fmicb.2017.00642

[…] denitrification genes under anaerobic conditions. involved promoter regions were deduced. these results were combined with a bioinformatical transcription factor binding site prediction using the virtual footprint tool of the prodoric database (münch et al., ). the expression of the napdaghbc operon was found induced by fnrl and significantly repressed by dnrd, dnre, and dnrf under anaerobic […]

PMCID: 5367854
PMID: 28119139
DOI: 10.1016/j.ymben.2017.01.009

[…] level (α-value) was set at 0.05., the c. pasteurianum genome was analysed for the presence of rex binding boxes using the rex box consensus sequence (5’-ttgttaannnnttaacaa) reported by with the ’virtual footprint’ algorithm () allowing 2 mismatches in a similar fashion to . as the c. pasteurianum genome was not available in the prodoric database () to which ’virtual footprint’ is linked, […]

PMCID: 5291005
PMID: 28217122
DOI: 10.3389/fmicb.2017.00145

[…] elements containing arg box motifs were identified by searching the l. monocytogenes genome with a position weight matrix derived from known e. coli argr recognition elements (), using the virtual footprint software program ()., the temperature-sensitive pksv7 shuttle vector was used for generating mutations in l. monocytogenes 10403s. a homologous recombination strategy […]

PMCID: 5458455
PMID: 28127899
DOI: 10.1002/mbo3.442

[…] region was identified using bprom (http://linux1.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb) (solovyev & salamov, )., binding site prediction: bprom and virtual footprint (http://www.prodoric.de/vfp/vfp_promoter.php) were used to identify the putative fur‐binding site within shut (münch et al., ; solovyev & salamov, )., rna structure prediction: […]


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Virtual Footprint institution(s)
Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany; Institute of Biochemical Engineering, Technical University Braunschweig, Braunschweig, Germany; Department of Informatics, University of Applied Sciences Wolfenbuttel, Wolfenbuttel, Germany
Virtual Footprint funding source(s)
Supported by the German Federal Ministry of Education and Research (BMBF) for the Bioinformatics Competence Center ‘Intergenomics’ (Grant No. 031U110A/031U210A).

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