All the tools you need to analyse your miRNAs


Target Prediction

TargetScan predicts biological targets of miRNAs by searching for the presence of 8mer, 7mer, and 6mer sites that match the seed region of each miRNA. As an option, only conserved sites are predicted. Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing and centered sites. In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using cumulative weighted context++ scores of the sites. As an option, predictions are also ranked by their probability of conserved targeting. TargetScanHuman considers matches to human 3' UTRs and their orthologs, as defined by UCSC whole-genome alignments. Conserved targeting has also been detected within open reading frames (ORFs). Compared to previous releases, Release 7 uses an improved method to predict targeting efficacy (the context++ model), uses 3' UTR profiles that indicate the fraction of mRNA containing each site, and uses updated miRNA families.

Homepage: Link

Last Software Update: June 1, 2016
Publication Date: Aug. 12, 2015
Citations: 2859 [via Pubmed]

Organism Specific:
  • human
  • mouse
  • fly
  • worm
  • fish

  • Reference Genome Needed:
    Online/Local: /
    Installation/User Level: easy (online), advanced (local)
    User Adjustability:
    User support:
    Precomputed Target Results Available For Download:
    Performance : False-positive predictions: 16%
  • miRBase

  • Target Prediction
    Algorithm Features:
  • seed match
  • conservation
  • free energy
  • site accessibility
  • target-site abundance
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content

  • Target Region: 3' UTR, CDS
    Target Annotation:
    NGS Data Needed:

    Comments & Ratings