BioProspector statistics

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Citations per year

Number of citations per year for the bioinformatics software tool BioProspector
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Tool usage distribution map

This map represents all the scientific publications referring to BioProspector per scientific context
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Associated diseases

This word cloud represents BioProspector usage per disease context
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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

Versioning


No version available

Publication for BioProspector

BioProspector citations

 (64)
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The SCO4117 ECF Sigma Factor Pleiotropically Controls Secondary Metabolism and Morphogenesis in Streptomyces coelicolor

2018
Front Microbiol
PMCID: 5826349
PMID: 29515563
DOI: 10.3389/fmicb.2018.00312
call_split See protocol

[…] 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 it […]

library_books

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

2018
Nucleic Acids Res
PMCID: 5934673
PMID: 29385521
DOI: 10.1093/nar/gky027

[…] in 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, the […]

library_books

PISMA: A Visual Representation of Motif Distribution in DNA Sequences

2017
Bioinform Biol Insights
PMCID: 5390925
PMID: 28469418
DOI: 10.1177/1177932217700907

[…] r understanding of gene regulatory networks and protein function. Many algorithms and computational tools have been designed to solve the motif-finding problem. Several of these tools are as follows: BioProspector, CompareProspector, and MDscan; MEME; info-gibbs; BAMBI; BEST; GAME; GALF-P; and Hegma. However, most of them are devoted to looking for regulatory motif prediction in more than 1 nucleo […]

library_books

An integrative and applicable phylogenetic footprinting framework for cis regulatory motifs identification in prokaryotic genomes

2016
BMC Genomics
PMCID: 4977642
PMID: 27507169
DOI: 10.1186/s12864-016-2982-x

[…] We compared the prediction of MP3 with six de novo motif finding tools: BOBRO, MDscan, Bioprospector, MEME, CONSENSUS, CUBIC, and MicroFootprinter. MicroFootprinter is designed for phylogenetic footprinting on prokaryotic genomes and can generate orthologous promoters on its web-server; […]

library_books

Genome Wide De Novo Prediction of Cis Regulatory Binding Sites in Mycobacterium tuberculosis H37Rv

2016
PLoS One
PMCID: 4757040
PMID: 26886880
DOI: 10.1371/journal.pone.0148965

[…] entation in the dataset. Secondly, Midha et al. used only one motif finding tool (MEME) to uncover motifs, whereas we included, in addition to MEME, four other complementary motif-finding algorithms (BioProspector, CUBIC, MDscan and MotifSampler) in our analyses. These five algorithms exhibit complementary prediction effect and collectively lead to more accurate prediction of true binding sites [] […]

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Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors

2016
Nucleic Acids Res
PMCID: 4797297
PMID: 26843427
DOI: 10.1093/nar/gkw051
call_split See protocol

[…] re managed by a PostgreSQL relational database system. Web applications were developed on an Apache Tomcat web server. Software for data processing and drawing maps were written in gcc, Perl or Java. BioProspector and WebLogo, furnished under the MIT license, can be used to analyze the consensus sequence of each TF. […]


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

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