BPROM protocols

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

 (10)
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/) [24]. 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/) [25]. comparison of pp3-related cluster […]

2017
PMCID: 5391158
PMID: 28435299
DOI: 10.2147/AABC.S117707

[…] these procedures were according to state of the art techniques and are described in “results and discussion” section., programs used for sequence alignments were blastp, clustal omega,31 genedoc,32 bprom (softberry),33 pepper34 and isfinder.35 phylogenetic tree construction was done by using the phylogeny.fr website.36 analysis of nrps sequences was done using online tools […]

2017
PMCID: 5655121
PMID: 29104571
DOI: 10.3389/fmicb.2017.02054

[…] hyp biosynthetic gene clusters in the genome of h. halophilus were identified using blastx and blastn and their transcriptional promoters and terminators were predicted using the web-based programs, bprom and findterm, respectively, available at http://www.softberry.com/., h. halophilus dsm 2266 cells were cultivated in mb containing different nacl concentrations (0.4, 1.0, 1.5, 2.0, 2.5, or 3.0 […]

2017
PMCID: 5716572
PMID: 29206865
DOI: 10.1371/journal.pone.0188998

[…] and for phylogenetic analyses of the proteins encoded by kdp operon of d. radiodurans. presence of e. coli like gene promoter elements in the upstream sequence of kdp operon was analyzed using bprom software [39]. phobius software was used to predict presence of a transmembrane domain in kdpb protein [40]., to ascertain if the kdp operon of d. radiodurans responds to k+ limitation, […]

2017
PMCID: 5744064
PMID: 29312251
DOI: 10.3389/fmicb.2017.02573

[…] its homologs were conducted using clustal omega1. the iscr-binding site was analyzed by the online program meme2 (bailey and elkan, 1994). the -35 and -10 sequences were predicted using softberry bprom tool3 (solovyev and salamov, 2011)., the iscr-mutant strain iscr-280 and its complemented strain iscr-280c were generated in our previous study (liu h.l. et al., 2015). to create a czor-mutant […]

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