PREDetector protocols

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PREDetector specifications

Information


Unique identifier OMICS_13575
Name PREDetector
Interface Web user interface
Restrictions to use License purchase required
Programming languages R
Database management system SQLite
Computer skills Basic
Version 2.0
Stability Beta
Maintained No

Maintainer


This tool is not available anymore.

Publication for PREDetector

PREDetector in pipeline

2008
PMCID: 2475637
PMID: 18515344
DOI: 10.1093/nar/gkn339

[…] a dna sequence logo describing the binding motif was then generated using weblogo (http://weblogo.berkeley.edu/). for rutr, each of the 20 binding sites identified by chip-chip were aligned in predetector () and a position weight matrix (pwm) was generated to describe the information content of the binding site. each target was then assigned a score depending on how it matched the pwm. […]


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PREDetector in publications

 (12)
PMCID: 5696649
PMID: 28945067
DOI: 10.1021/acschembio.7b00597

[…] measurement., the putative binding sites for the iron utilization regulator dmdr1 and for the arginine biosynthesis regulator argr were detected on the chromosome of streptomyces sp. mbt76 using the predetector software and according to the method described. for the generation of the dmdr1 position weight matrix (pwm), we used the sequence of the iron box which lies at position −82 nt upstream […]

PMCID: 5402319
PMID: 28484446
DOI: 10.3389/fmicb.2017.00736

[…] of wt gene transcripts under stress conditions (supplementary figure ), leading to the putative -35 and -10 promoter sequences shown in figure . analysis of these promoter sequences using the predetector web-based program revealed a consensus sequence bgvnvh-n15-gsnnhh (figure ), which resembles that of σb-specific promoters of s. coelicolor (gnntn-n14-16-gggtay) (y: c or t) ()., rna […]

PMCID: 4890002
PMID: 27250236
DOI: 10.1038/srep27144

[…] homologues used for the analysis are listed in the legend of . the new cebr position weight matrix (see ) was created using dna motifs known to be bound by cebr in s. griseus and s. scabies with the predetector software and the prediction of the cebr regulon was performed according to the philosophy described previously. graphpad prism 5 software was used to determine binding parameters of cebe […]

PMCID: 4865122
PMID: 27171430
DOI: 10.1371/journal.pone.0155396

[…] and rcryst was calculated for the remaining reflections., b determined using molprobity., to assess the dna binding ability of the purified bhargr, we predicted dna operator sequences by using the predetector program [] based on the argr/ahrc recognition signal candidate sequences []. a 119-bp cognate dna containing its own promoter region was prepared by polymerase chain reaction (pcr) using […]

PMCID: 4856308
PMID: 27145180
DOI: 10.1371/journal.pone.0153249

[…] the knowledge of two genuine binding sites of rokb facilitated a wider search for further binding sites in the genome of s. coelicolor to identify possible members of the rokb regulon. the program predetector [] was used to generate a matrix based on the two newly identified binding sites, which was then applied to a genome-wide search for further binding sites. the seven hits with the highest […]


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PREDetector institution(s)
InBioS - PhytoSYSTEMS, University of Liège, Liège, Belgium; Hedera-22 SCRL, Esneux, Belgium; InBioS - Center for Protein Engineering, University of Liège, Liège, Belgium; Systems and Modeling - Montefiore Institute, University of Liège, Liège, Belgium; Microbial Biotechnology - Institute of Biology, Leiden University, Leiden, Netherlands
PREDetector funding source(s)
This work is supported by a First Spin-off grant from the Walloon Region [Grant number: 1510530; FSO AntiPred].

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