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Protocols

BioProspector specifications

Information


Unique identifier OMICS_06283
Name BioProspector
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for BioProspector

BioProspector citations

 (99)
library_books

The SCO4117 ECF Sigma Factor Pleiotropically Controls Secondary Metabolism and Morphogenesis in Streptomyces coelicolor

2018
PMCID: 5826349
PMID: 29515563
DOI: 10.3389/fmicb.2018.00312

[…] were grouped into 33 putative operons (supplementary table ). a library of putative regulatory sequences has compiled from the 250 nucleotide-long sequences located upstream of the putative operons. bioprospector (liu et al., ) was used to search for bipartite overrepresented motifs in these sequences. searches were performed only in the forward strand, and the following parameters were varied […]

library_books

Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets

2018
PMCID: 5934673
PMID: 29385521
DOI: 10.1093/nar/gky027

[…] dimers was introduced, with an entropy minimization learning algorithm bipad/maskminent (). discovery of spaced dyads (pairs of relatively short motifs) was considered in (,). gibbs sampling based bioprospector () is another early dimer search algorithm. recent dimer prediction methods include spamo (), itfs (), and taco (). all start from given monomeric ppms and find, using thresholding, […]

library_books

Komodo dragon inspired synthetic peptide DRGN 1 promotes wound healing of a mixed biofilm infected wound

2017
PMCID: 5445593
PMID: 28649410
DOI: 10.1038/s41522-017-0017-2

[…] this bacteria-laden saliva never sickens the komodo dragon. investigators therefore hypothesized that proteins in the dragon's saliva or blood might provide immunity. using our amp discovery bioprospector platform, we identified a komodo dragon peptide from komodo plasma that we named vk25 (fig. s). inspired by this vk25 peptide, we designed and created a new short synthetic peptide, […]

library_books

CTCF interacts with the lytic HSV 1 genome to promote viral transcription

2017
PMCID: 5206630
PMID: 28045091
DOI: 10.1038/srep39861

[…] neighboring genes., ctcf is known to interact with the host genome through a consensus sequence, and it is unknown whether ctcf interacts with the hsv-1 genome through a similar mechanism. using bioprospector software, we found that the ctcf binding consensus from these peaks are highly similar to the known ctcf binding motif (). among the 25 peaks, 15 are motif positive ( red numbered […]

library_books

Modeling the cis regulatory modules of genes expressed in developmental stages of Drosophila melanogaster

2017
PMCID: 5452948
PMID: 28584716
DOI: 10.7717/peerj.3389

[…] (2) feature-computation, and (3) model-construction. the motif-prediction subset was used to predict de novo motifs. in the motif discovery step, we run four algorithms: meme (), weeder (), bioprospector () and motifsampler (). redundant motifs were compared with the algorithm tomtom () and removed by retaining the motif with higher information content in each pair of matched motifs. […]

library_books

CELF1 is a central node in post transcriptional regulatory programmes underlying EMT

2016
PMCID: 5121338
PMID: 27869122
DOI: 10.1038/ncomms13362

[…] via quantitative real-time pcr (qrt-pcr; )., the potential contribution of a given transcript′s 3′-utr to the stability and translation of the mrna is well established. we thus used the meme and bioprospector algorithms to identify enriched 6–10 nucleotide motifs within the 3′-utrs of polysomally enriched and depleted transcripts. both analyses revealed strong enrichment (meme p=3.1e−34) […]


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BioProspector institution(s)
Stanford Medical Informatics, Stanford University, Stanford, CA, USA

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