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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 citations

 (33)
library_books

The redox sensing protein Rex modulates ethanol production in Thermoanaerobacterium saccharolyticum

2018
PLoS One
PMCID: 5886521
PMID: 29621294
DOI: 10.1371/journal.pone.0195143

[…] n 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 s […]

call_split

Identification and characterization of preferred DNA binding sites for the Thermus thermophilus transcriptional regulator FadR

2017
PLoS One
PMCID: 5597230
PMID: 28902898
DOI: 10.1371/journal.pone.0184796
call_split See protocol

[…] ction while mapping these sites to specific gene promoters was performed using the BLASTn-embedded Nucleotide Graphics function.Comparative genomics regulon inference analysis was performed using the RegPredict webserver (http://regpredict.lbl.gov/regpredict/), selecting the full set of Deinococcus-Thermus genomes, and determining regulon inference by known PWM using a training set composed of the […]

library_books

The Role of the Regulator Fur in Gene Regulation and Virulence of Riemerella anatipestifer Assessed Using an Unmarked Gene Deletion System

2017
PMCID: 5609570
PMID: 28971067
DOI: 10.3389/fcimb.2017.00382

[…] 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 bindin […]

library_books

Genomic Reconstruction of Carbohydrate Utilization Capacities in Microbial Mat Derived Consortia

2017
Front Microbiol
PMCID: 5507952
PMID: 28751880
DOI: 10.3389/fmicb.2017.01304

[…] truction 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 c […]

library_books

LdtR is a master regulator of gene expression in Liberibacter asiaticus

2017
PMCID: 5481520
PMID: 28503858
DOI: 10.1111/1751-7915.12728

[…] arallel to the RNA‐seq assay, we performed a genome‐wide in silico analysis in L. asiaticus to identify potential LdtR binding sequences. This search was accomplished using the computational platform RegPredict (Novichkov et al., ). The software was directed to identify sequences with high similarity to the LdtR binding motif (5’ ATATTCCTTGTATTTTAA 3’) determined earlier by DNase I footprinting (P […]

library_books

A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea

2017
Nucleic Acids Res
PMCID: 5397151
PMID: 28073944
DOI: 10.1093/nar/gkw1331

[…] ntification of candidate RbkR-binding site motifs and regulon reconstructions, we used a previously established comparative genomics approach () implemented in the Genome Explorer software () and the RegPredict Web server tool (). We started regulon reconstruction from collection of initial training sets of known genes involved in RBP and/or vitamin B2 transport in each archaeal lineage containing […]

Citations

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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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