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BioVLAB-MMIA-NGS


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


Analysis Scheme:
BioVLAB-MMIA-NGS is Cloud-based miRNA mRNA integraed analysis system using NGS data. System computes differentially/significantly expressed miRNAs (DEmiRNAs) and mRNAs/genes (DEGs), and with targeting information, DEGs targeted by DEmiRNAs and having negative correlation between them are extracted.

Homepage: Link

Last Software Update: Sept. 29, 2014
Publication Date: Sept. 29, 2014
Reference: [Journal] [Pubmed] [CrossRef]
Citations: 8 [via Pubmed]

Organism Specific:
  • human
  • mice
  • macaca
  • plants (rice)

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

    • 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:
    Target Enrichment Analysis:
    NGS Data Needed:
    Metaserver:
    Target Prediction Methods Used For Metaserver:
  • TargetScan
  • PITA
  • miRanda

    • 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
    Novel miRNA / Precursor Analysis: Prediction
    NGS Data Needed:
    Differential Expression Analysis
    Algorithm: DESeq, Cufflinks, Limma
    miRNA differential expression:
    mRNA differential expression:
    NGS Data Needed:
    Target Functional Analysis
    Algorithm: DAVID software
    Analysis Features:
  • GO Terms
  • KEGG Pathways
  • miRNA/mRNA Correlation
    • NGS Data Needed:
    Target Prediction Data Needed:
    Known miRNA Identification
    NGS Data Needed:





    Comments & Ratings
    • zahid bhat Thu 20 Aug 2020 10:21
      good