RegPredict specifications

Information


Unique identifier OMICS_24441
Name RegPredict
Software type Application/Script
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No

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Publication for RegPredict

RegPredict in publications

 (30)
PMCID: 5892913
PMID: 29634775
DOI: 10.1371/journal.pone.0195746

[…] []. although ldtr in vivo modulates the expression of znua2 and znua3 homologues in l. crescens [], it was found that ldtr only bound to pznua2 and not to pznua1 from l. asiaticus (). using regpredict [], two ldtr binding boxes were identified within pznua2; the first located between the bases -28(tattttattaaa-n5-tataattgaata)+1, and the second located between the bases […]

PMCID: 5886521
PMID: 29621294
DOI: 10.1371/journal.pone.0195143

[…] the ravcheev et al. study included three genomes (t. ethanolicus, thermoanaerobacter tengcongensis, and caldicellulosiruptor saccharolyticus), and putative rex-binding sites were predicted with the regpredict web server tool (regpredict.lbl.gov) []. in this study, we utilized a different site-prediction platform patloc (http://www.cmbl.uga.edu/software/patloc.html) to find putative rex-binding […]

PMCID: 5597230
PMID: 28902898
DOI: 10.1371/journal.pone.0184796

[…] translation start sites., (–) orthologous sequences not found., to better identify fadr-regulated operons in other organisms, a comparative genomics regulon inference analysis was performed using regpredict, available deinococcus-thermus genomes, and a profile built from a training set composed of the fadr binding sequences present in the repsa-identified promoters []. additional parameters […]

PMCID: 5609570
PMID: 28971067
DOI: 10.3389/fcimb.2017.00382

[…] proteins (table )., the putative fur binding sequence and the distance from the start condon of the genes regulated by fur is shown in table . promoter sequences were analyzed using software regpredict and clustalw for identification of putative binding sequence of fur protein which was 19 bp long and sequence was predicted as 5′-atttagaattattctaaat-3′ (figure ). therefore, the fur […]

PMCID: 5507952
PMID: 28751880
DOI: 10.3389/fmicb.2017.01304

[…] of novel tf regulons, we used the bioinformatics technique based on identification and comparative analysis of candidate tf-binding sites in closely related genomes () and implemented in the regpredict software (). this approach includes the following steps: (i) search for orthologous groups of the studied tfs in other reference genomes; (ii) selection of conserved orthologous gene loci […]


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RegPredict institution(s)
Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Burnham Institute for Medical Research, La Jolla, CA, USA; Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia; Department of Bioengineering, University of California, Berkeley, CA, USA; Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
RegPredict funding source(s)
Supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics Program: GTL through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the US Department of Energy; National Science Foundation (award DBI-0850546); Howard Hughes Medical Institute (55005610); Russian Foundation for Basic Research (08-04-01000, 09-04-92745, 10-04-01768, 09-04-92742); Russian Academy of Sciences (program ‘Molecular and Cellular Biology’); Federal Agency on Education (P2581); Russian Science Agency (contract 2.740.11.0101); and Russian President’s grant for young scientists (MK-422.2009.4).

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