All the tools you need to analyse your miRNAs

mirTools 2.0

Target Prediction Novel miRNA/Precursor Prediction Sequencing Analysis Target Functional Analysis Differential Expression Analysis Known miRNA Identification All in 1 Tools IsomiRs Identification

Analysis Scheme:
MirTools 2.0 is updated version of mirTools, which was developed to comprehensive characterize the small RNA transcriptome obtained from high-throughput sequencing. It enables user to: detect and profile non-coding RNA (tRNA, snRNA, snoRNA, rRNA ans piRNA); obtain detailed annotation ifmromation about known miRNA (absolute/realtive reds count and most abundant tags); identify the microRNA targeted genes and their detailed functional annotate; perform the comparison of many samples and identify the differentially expressed non-coding RNAs between experimental groups; discovery the novel miRNAs.

Homepage: Link

Last Software Update: March 11, 2013
Publication Date: May 29, 2013
Citations: 40 [via Pubmed]

Organism Specific:
  • human
  • mouse
  • rat
  • chicken
  • fish
  • worm
  • fly
  • other animals (selectable)
  • plants (selectable)
  • any (local)

  • Reference Genome Needed: (online) / (local)
    Online/Local: /
    Installation/User Level: easy
    User Adjustability:
    User support:
    Precomputed Target Results Available For Download:
    Target Prediction
    Algorithm Features:
  • seed match
  • conservation
  • free energy
  • site accessibility
  • machine learning
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content

  • Target Region: 3'UTRS, CDS
    Target Annotation:
    NGS Data Needed:
    Target Prediction Methods Used For Metaserver:
  • RNAhybrid
  • MicroCosm
  • microT_v3.0
  • miRanda
  • miRNAMap
  • MirTarget2
  • TargetScan
  • TargetSpy

  • Sequencing Analysis
    Algorithm Features:
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • target prediction
  • target annotation
  • precursor prediction
  • isomiRs identyfication
  • other ncRNA identification

  • Sequencing Platform Specific: Illumina
    PARE/CLIP-Seq: /
    Novel miRNA/Precursor Prediction
    Prediction Features:
  • sequence
  • structure
  • conservation

  • Algorithm: miRDeep, MIREAP
    Novel miRNA / Precursor Analysis: Prediction
    NGS Data Needed:
    Differential Expression Analysis
    Algorithm: Wilcoxon Rank-sum test, Bayesian method
    miRNA differential expression:
    mRNA differential expression:
    NGS Data Needed:
    Target Functional Analysis
    Algorithm: hypergeometric test
    Analysis Features:
  • GO Terms
  • KEGG Pathways
  • Protein-Protein Interaction
  • NGS Data Needed:
    Target Prediction Data Needed:
    Known miRNA Identification
    NGS Data Needed:
    IsomiRs Identification
    NGS Data Needed:

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