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plantDARIO


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


Analysis Scheme:
plantDARIO is a free web service focussing on the analysis of short-read data from small RNA-seq experiments in plants. It provides basic features including quality control, read normalization, ncRNA quantification, and prediction of putative novel ncRNAs. At present Arabidopsis thaliana, Beta vulgaris, and Solanum lycopersicum are covered.

Homepage: Link

Last Software Update: Dec. 23, 2014
Publication Date: Dec. 23, 2014
Reference: [Journal] [Pubmed] [CrossRef]
Citations: 6 [via Pubmed]

Organism Specific:
  • plants

    • Reference Genome Needed:
    Online/Local: /
    Installation/User Level: easy
    User Adjustability:
    User support:
    Precomputed Target Results Available For Download:
    Input Data Required:
  • mapped reads/tags and/or the user annoated loci stored in the bed format

    • Cross-Refferences:
  • Ensembl

    • Sequencing Analysis
    Algorithm Features:
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • other ncRNA identification

    • Sequencing Platform Specific: Any
    PARE/CLIP-Seq: /
    Novel miRNA/Precursor Prediction
    Prediction Features:
  • sequence
  • structure
  • miRNA/miRNA* position prediction

    • Algorithm: NOVOMIR
    Novel miRNA / Precursor Analysis: Classification
    NGS Data Needed:
    Differential Expression Analysis
    miRNA differential expression:
    mRNA differential expression:
    NGS Data Needed:
    Known miRNA Identification
    NGS Data Needed:





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