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BPROM specifications


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


BPROM citations


Random sequences rapidly evolve into de novo promoters

Nat Commun
PMCID: 5906472
PMID: 29670097
DOI: 10.1038/s41467-018-04026-w

[…] s of 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 a […]


The higBA Toxin Antitoxin Module From the Opportunistic Pathogen Acinetobacter baumannii – Regulation, Activity, and Evolution

Front Microbiol
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 have an […]


Identification of novel MITEs (miniature inverted repeat transposable elements) in Coxiella burnetii: implications for protein and small RNA evolution

BMC Genomics
PMCID: 5896051
PMID: 29642859
DOI: 10.1186/s12864-018-4608-y
call_split See protocol

[…] n order to demonstrate the potential for transcription of QMITE inserts, prediction of sigma-70 consensus promoter elements and Rho factor-independent terminators in QMITE inserts was performed using BPROM (http://www.softberry.com/berry.phtml?topic=bprom&group =programs&subgroup=gfindb) and ARNold (http://rna.igmors.u-psud.fr/toolbox/arnold/), respectively. CIRCOS software [] (http://circos.ca/so […]


Genomic Characterization of Sixteen Yersinia enterocolitica Infecting Podoviruses of Pig Origin

PMCID: 5923468
PMID: 29614052
DOI: 10.3390/v10040174

[…] of T7-like phages genomes carry promoters used by the host RNAP upon the entry of the phage DNA into the host cytoplasm []. In the fPS-phages, three to six host RNAP promoters were identified by the BPROM program (). As expected, the identified promoters were all located upstream of g002 encoding the phage RNAP. Altogether 11 to 13 putative phage RNAP specific 23 bp long promoter sequences were i […]


Three Hcp homologs with divergent extended loop regions exhibit different functions in avian pathogenic Escherichia coli

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

[…] he orphan hcp2B-vgrG2 might be regulated by a specific mechanism.Fig. 3It 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 operon […]


Controlled branched chain amino acids auxotrophy in Listeria monocytogenes allows isoleucine to serve as a host signal and virulence effector

PLoS Genet
PMCID: 5864092
PMID: 29529043
DOI: 10.1371/journal.pgen.1007283
call_split See protocol

[…] 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 o […]


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