BioProspector 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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Maintainer


  • person_outline Jun S. Liu <>

Publication for BioProspector

BioProspector IN pipelines

 (3)
2012
PMCID: 3441632
PMID: 23028346
DOI: 10.1371/journal.pgen.1002929

[…] sphaeroides 2.4.1 were obtained from vimss microbesonline (http://www.microbesonline.org/operons/) [26]. the promoter sequences predicted to be recognized by rpohi and rpohii were discovered using bioprospector [48] set to search for bi-partite conserved sequence motifs. the promoter sequence alignments were refined using hmmer 1.8.5 [49]. the logo representations of the promoter sequence […]

2008
PMCID: 2475637
PMID: 18515344
DOI: 10.1093/nar/gkn339

[…] as the centre of the probe within the peak that had the highest cy5/cy3 signal. figure 1., the rutr-binding motif was extracted from 500-bp dna sequences centred around the binding peaks using bioprospector (http://ai.stanford.edu/~xsliu/bioprospector/). a dna sequence logo describing the binding motif was then generated using weblogo (http://weblogo.berkeley.edu/). for rutr, […]

2008
PMCID: 2475637
PMID: 18515344
DOI: 10.1093/nar/gkn339

[…] that had the highest cy5/cy3 signal. figure 1., the rutr-binding motif was extracted from 500-bp dna sequences centred around the binding peaks using bioprospector (http://ai.stanford.edu/~xsliu/bioprospector/). a dna sequence logo describing the binding motif was then generated using weblogo (http://weblogo.berkeley.edu/). for rutr, each of the 20 binding sites identified by chip-chip […]

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

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