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sRNAtoolbox


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


Analysis Scheme:
sRNAtoolbox is aimed to provide small RNA researchers with several useful tools including sRNA expression profiling from deep sequencing experiments and several downstream analysis tools. The center piece of sRNAtoolbox is sRNAbench, which allows the expression profiling and prediction of novel microRNAs in deep sequencing experiments. The other tools can be either launched on sRNAbench results, or independently using the appropriate file formats.

Homepage: Link

Last Software Update: May 2, 2015
Publication Date: May 27, 2015
Reference: [Journal] [Pubmed] [CrossRef]
Citations: 118 [via Pubmed]

Organism Specific:
  • human
  • mouse
  • rat
  • chicken
  • fly
  • fish
  • viruses
  • plants (selectable)
  • bacteria
  • other animals (selectable)

    • Reference Genome Needed:
    Online/Local: /
    Installation/User Level: easy
    User Adjustability:
    User support:
    Precomputed Target Results Available For Download:
    Cross-Refferences:
  • NCBI

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

    • Target Region: 3' UTR, CDS
    Target Annotation:
    NGS Data Needed:
    Metaserver:
    Target Prediction Methods Used For Metaserver:
  • TAPIR
  • psRobot
  • miRanda
  • PITA
  • TargetSpy

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

    • Sequencing Platform Specific: Illumina, SOLiD
    PARE/CLIP-Seq: /
    Novel miRNA/Precursor Prediction
    Prediction Features:
  • sequence
  • structure
  • reads cluster analysis

    • Novel miRNA / Precursor Analysis: Prediction
    NGS Data Needed:
    Differential Expression Analysis
    Algorithm: DESeq, NOISeq, edgeR
    miRNA differential expression:
    mRNA differential expression:
    NGS Data Needed:
    Target Functional Analysis
    Algorithm: Annotation-Modules tool
    Analysis Features:
  • GO Terms
    • NGS Data Needed:
    Target Prediction Data Needed:
    Known miRNA Identification
    NGS Data Needed:
    IsomiRs Identification
    NGS Data Needed:





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