All the tools you need to analyse your miRNAs

wapRNA


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


Analysis Scheme:
wapRNA provides an integrated tool for RNA sequence, refers to the use of High-throughput sequencing technologies to sequence cDNAs in order to get information about a sample's RNA content. wapRNA provides researchers with efficient ways to measure RNA sequence experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identifying gene fusions, annotate the known miRNAs or predict the news and so on. 

Homepage: Link

Last Software Update: July 21, 2011
Publication Date: Sept. 6, 2011
Citations: 23 [via Pubmed]

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

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

  • Target Prediction
    Algorithm Features:
  • seed match
  • conservation
  • free energy
  • target-site abundance
  • 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:
  • RNAhybrid
  • miRanda

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

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

  • Algorithm: miRDeep
    Novel miRNA / Precursor Analysis: Prediction
    NGS Data Needed:
    Differential Expression Analysis
    Algorithm: DEGseq
    miRNA differential expression:
    mRNA differential expression:
    NGS Data Needed:
    Target Functional Analysis
    Analysis Features:
  • GO Terms
  • KEGG Pathways
  • NGS Data Needed:
    Target Prediction Data Needed:
    Known miRNA Identification
    NGS Data Needed:





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