All the tools you need to analyse your miRNAs

MTide


Target Prediction Novel miRNA/Precursor Prediction Sequencing Analysis Target Functional Analysis Differential Expression Analysis Known miRNA Identification


Analysis Scheme:
MTide is an integrated pipeline designed to parse sRNA-seq and degradome data for miRNA-target identification in plant. It can quantify the known miRNA expression and identify novel miRNA from sRNA-seq data, identify the target of miRNA from degradome data signature, predict target of miRNA precisely, prioritize predicted target according to GO similarity to known or validated target, and identify the expressed miRNA between two samples.

Homepage: Link

Last Software Update: June 13, 2014
Publication Date: Sept. 24, 2014
Citations: 17 [via Pubmed]

Organism Specific:
  • plants

  • Reference Genome Needed:
    Online/Local: /
    Installation/User Level: advanced
    User Adjustability:
    User support:
    Precomputed Target Results Available For Download:
    Target Prediction
    Algorithm Features:
  • seed match
  • conservation
  • free energy
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • degradome seq analysis

  • Target Region: 3'UTR
    Target Annotation:
    Algorithm: TAPIR, CleaveLand4
    NGS Data Needed:
    Metaserver:
    Sequencing Analysis
    Algorithm Features:
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • target prediction
  • target annotation
  • precursor prediction

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

  • Algorithm: miRDeep2 method
    Novel miRNA / Precursor Analysis: Prediction
    NGS Data Needed:
    Differential Expression Analysis
    Algorithm: DESeq
    miRNA differential expression:
    mRNA differential expression:
    NGS Data Needed:
    Target Functional Analysis
    Analysis Features:
  • GO Terms
  • NGS Data Needed:
    Target Prediction Data Needed:
    Known miRNA Identification
    NGS Data Needed:





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