BPROM protocols

View BPROM computational protocol

BPROM statistics

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Associated diseases

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BPROM specifications

Information


Unique identifier OMICS_17959
Name BPROM
Interface Web user interface
Restrictions to use None
Input data A nucleotide sequence.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


BPROM in pipelines

 (28)
2018
PMCID: 5780444
PMID: 29403457
DOI: 10.3389/fmicb.2018.00002

[…] in the r/bioconductor package “gplots”., the upstream regions of all phage genes (300 bp) were collected from the ma-lmm01 genome. the primary sigma factor recognition sequences were predicted using bprom with default parameters. the promoter sequences were aligned separately for each motif (-10 box and -35 box) using clustalw (). logos were prepared using weblogo ()., rna-seq results […]

2018
PMCID: 5822837
PMID: 29479501
DOI: 10.7717/peerj.4402

[…] tools were used on specific contigs where ter genes were found (liqb01000002.1, position 189803-204267; liqb01000003.2, position 286133-301767): prompredict algorithm and the online program bprom (; http://www.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb). both results were jointly analyzed., to investigate if the presence and number of ter genes […]

2018
PMCID: 5923468
PMID: 29614052
DOI: 10.3390/v10040174

[…] using arnold software (http://rna.igmors.u-psud.fr/). the promoter consensus sequences were generated using the sequence logo generator (weblogo) []. the host rnap promoters were identified using bprom []. all the identified promoter and terminator sequences were further verified manually using the artemis. the phylogenetic trees for the amino acid sequences of the dna ligase, rnap, […]

2017
PMCID: 5327559
PMID: 28241831
DOI: 10.1186/s12934-017-0651-7

[…] quick response to cope with environmental changes such as nutrient deprivation. to find if these alternative factors are being used for the upregulation of the r. jostii genes in mmgln, the program bprom (http://www.softberry.com/) for the recognition of sigma70 promoters was used with the 150 bp immediately upstream from each orf start. a putative sigma70 binding site was found […]

2017
PMCID: 5367828
PMID: 28346467
DOI: 10.1371/journal.pone.0174429

[…] offered by ncbi (http://www.ncbi.nlm.nih.gov/blast) and the pseudomonas genome database (http://www.pseudomonas.com/) []. the putative promoter upstream of the attachment site was predicted by bprom (http://www.softberry.com/berry.phtml). the circular map of the pa1 genome was generated using cgview (http://wishart.biology.ualberta.ca/cgview/) []. comparison of pp3-related cluster […]


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BPROM in publications

 (204)
PMCID: 5906472
PMID: 29670097
DOI: 10.1038/s41467-018-04026-w

[…] the e. coli genome by recoding each of its genes, while preserving the wt amino-acid sequence and the overall codon bias (methods)., our main method to identify promoters inside genes was based on bprom,, an available software for promoter detection in e. coli that takes into account not only the −10 and −35 elements but also other factors that affect transcription level, like the tgn element […]

PMCID: 5906591
PMID: 29706946
DOI: 10.3389/fmicb.2018.00732

[…] toxin is the first gene in the operon, regulate their toxin:antitoxin ratio. we looked if an additional promoter could be found for higaab, indicating additional regulation for antitoxin expression. bprom tool () predicted promoter elements (-10 and -35) upstream the higba2ab operon and higa2ab coding sequence (figure ), indicating that besides promoter for the operon, higa2ab might also […]

PMCID: 5923468
PMID: 29614052
DOI: 10.3390/v10040174

[…] using arnold software (http://rna.igmors.u-psud.fr/). the promoter consensus sequences were generated using the sequence logo generator (weblogo) []. the host rnap promoters were identified using bprom []. all the identified promoter and terminator sequences were further verified manually using the artemis. the phylogenetic trees for the amino acid sequences of the dna ligase, rnap, […]

PMCID: 5874247
PMID: 29593238
DOI: 10.1038/s41426-018-0042-0

[…] orphan hcp2b-vgrg2 might be regulated by a specific mechanism.fig. 3, it is reasonable to infer that hcp2b-vgrg2 is controlled by different operons from the major cluster of t6ss2. prediction by the bprom program softberry followed by reverse transcription pcr indicated that hcp2b-xmtv forms one operon (fig. ) and thus shares a single promoter. a homolog of the duf2169 protein in the hcp2b […]

PMCID: 5864092
PMID: 29529043
DOI: 10.1371/journal.pgen.1007283

[…] plate reader at 37°c for 12 h. luminescence measurements at 12 h time point at the different bcaa concentrations were normalized to the corresponding od600., lm ilvd promoter was predicted using bprom []. the leader peptide was predicted using ape (http://biologylabs.utah.edu/jorgensen/wayned/ape). terminator and anti-terminator structures were predicted using pasific [], with the kind help […]


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