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PROGNOS specifications

Information


Unique identifier OMICS_10631
Name PROGNOS
Alternative name Predicted Report Of Genome-wide Nuclease Off-target Sites
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Bacteria
    • Escherichia coli
  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio

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Maintainer


  • person_outline Gang Bao <>

Information


Unique identifier OMICS_10631
Name PROGNOS
Alternative name Predicted Report Of Genome-wide Nuclease Off-target Sites
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Bacteria
    • Escherichia coli
  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio

Maintainer


  • person_outline Gang Bao <>

Publication for Predicted Report Of Genome-wide Nuclease Off-target Sites

PROGNOS in publications

 (39)
PMCID: 5955954
PMID: 29769555
DOI: 10.1038/s41598-018-25654-8

[…] lgb knockout cattle with the bovine reference genome to identify sequence variations that were then correlated with the juxtaposition of degenerate binding sites for each of our talen monomers using prognos. this identified a total of 316 potential off-target sites considering hetero- and homodimeric talen pairs. the distributions of these sites across the different degeneracy levels […]

PMCID: 5852297
DOI: 10.1016/j.omtn.2018.01.009

[…] c.6503_6511del9 (9-bp deletion) alleles in these cells ().figure 3, to assess the specificity of talens activity, we identified genomic sites with the potential for off-target cleavage by using the prognos software that ranks sites according to number of mismatches relative to the intended target sequence and repeat variable diresidue (rvd)-nucleotide binding frequencies. the presence of indel […]

PMCID: 5719732
PMID: 29212522
DOI: 10.1186/s13643-017-0649-6

[…] rule*) or (predict* and (outcome* or risk* or model*)) or ((history or variable* or criteria or scor* or characteristic* or finding* or factor*) and (predict* or model* or decision* or identif* or prognos*)) or (decision* and (model* or clinical* or logistic models/)) or (prognostic and (history or variable* or criteria or scor* or characteristic* or finding* or factor* or model*))) []., […]

PMCID: 5666315
PMID: 28899930
DOI: 10.15252/emmm.201707540

[…] two different pairs of primers for the 3′ or the 5′ integration junction were used ()., among the different aavs1 off‐targets that were identified by mussolino et al () using the bioinformatic tool prognos, we studied five that have also been experimentally validated: atrnl1, begain, chrac1, h19, and linc00548., genomic dna from cd34+ cells targeted with the pgk‐egfp idlv, together […]

PMCID: 5524345
PMID: 28738084
DOI: 10.1371/journal.pone.0181724

[…] of pcr products generated with primers ll (nt7259-nt7284) and rr (nt9058-nt9027) located 166 nt and 444 nt respectively, outside the hr region., predicted off-target sites were identified by prognos []. potential off-target sites were pcr amplified from liver gdna (founder #19) and cloned into the pcr4 vector (life technologies). eight to twelve independent clones of each potential […]


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PROGNOS institution(s)
Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
PROGNOS funding source(s)
National Institutes of Health (NIH Nanomedicine Development Center Award; grant number PN2EY018244); National Science Foundation Graduate Research Fellowship (DGE-1148903)

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