All the tools you need to analyse your miRNAs

CPSS


Target Prediction Novel miRNA/Precursor Prediction Sequencing Analysis Target Functional Analysis Differential Expression Analysis Known miRNA Identification All in 1 Tools IsomiRs Identification miRNA-SNP Analysis


Analysis Scheme:
CPSS is (a computational platform for the analysis of small RNA deep sequencing data), designed to completely annotate and functionally analyse microRNAs (miRNAs) from NGS data on one platform with a single data submission.

Homepage: Link

Last Software Update: Feb. 22, 2012
Publication Date: May 9, 2012
Citations: 20 [via Pubmed]

Organism Specific:
  • human
  • mouse
  • rat
  • chicken
  • fish
  • other animals (selectable)

  • Reference Genome Needed:
    Online/Local: /
    Installation/User Level: intermediate
    User Adjustability:
    User support:
    Precomputed Target Results Available For Download:
    Input Data Required:
  • NGS Data

  • 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
  • local AU content

  • Target Region: 3' UTR, CDS
    Target Annotation:
    NGS Data Needed:
    Metaserver:
    Target Prediction Methods Used For Metaserver:
  • miRanda
  • RNAhybrid
  • MicroCosm
  • miRNAMap
  • microTv3.0
  • TargetScan
  • MirTarget2
  • TargetSpy

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

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

  • Algorithm: miRDeep, mireap
    Novel miRNA / Precursor Analysis: Prediction
    NGS Data Needed:
    Differential Expression Analysis
    Algorithm: -
    miRNA differential expression:
    mRNA differential expression:
    NGS Data Needed:
    Target Functional Analysis
    Algorithm: Fisher's exact test
    Analysis Features:
  • GO Terms
  • KEGG Pathways
  • Protein-Protein Interaction
  • NGS Data Needed:
    Target Prediction Data Needed:
    miRNA-SNP Analysis
    Target Prediction Data Needed:
    NGS Data Needed:
    Known miRNA Identification
    NGS Data Needed:
    IsomiRs Identification
    NGS Data Needed:





    Comments & Ratings
    • pradyumna Jayaram Fri 03 Mar 2017 13:32
      The tool is not working anymore