BPROM pipeline

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

PMCID: 5443158

[…] (ncbi) database using the following entries: tpxd sequence gene id: 4441865. streptococcus pneumoniae d39 strain sequence id: nc_008533.1. promoter elements were predicted using the softberry bprom algorithm of bacterial promoters (http://www.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb). known cody-regulated genes in s. pneumoniae were retrieved […]

PMCID: 5367828

[…] 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 […]

PMCID: 5014404

[…] orfs in blastp (http://blast.ncbi.nlm.nih.gov/blast.cgi). the presence of transmembrane domains was verified with tmhmm software [34]. prokaryotic promoter regions were identified by using the bprom prediction program on the softberry website (http://www.softberry.com/). potential phage promoter sites were scanned for using phire software [35]. palindromic repeat regions were identified […]

PMCID: 4526809

[…] s each. all measurements were done in triplicate. the samples gave a clear signal (the y-intercept was 0.95) and required only moderate attenuation (set at 7)., promoter analysis was performed using bprom (solovyev and salamov, 2011). identification of rho-independent bacterial terminators was done using was done using arnold web tool (naville et al., 2011; […]

PMCID: 3080317

[…] presenting two tmd., no trna genes were predicted in the ϕibb-pf7a genome using trnascan-se. several potential putative promoters were identified in the dna sequence of ϕibb-pf7a, using phire and bprom (additional file 3, table s2). using strict criteria for the assignment of host promoter sites, i.e. that four out of the six bp in the -10 and -35 regions be conserved, two host-dependent […]

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