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sRNAtools


Target Prediction Sequencing Analysis Target Functional Analysis Differential Expression Analysis Known miRNA Identification IsomiRs Identification


sRNAtools can be used to identify and functionally annotate diverse kinds of sncRNA for up to 21 model species (including human, mouse, Arabidopsis, rice, etc.), including (i) profiling of miRNAs, Piwi-interacting RNA (piRNAs), piRNA-producing loci (piRNA cluster), tRNAs, natsiRNA, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs) and rRNAs and (ii) discovering isomiRs, novel miRNAs, tRFs, plant-specific 24-nt siRNAs and phasiRNAs. sRNAtools also provides web-based approaches to detect sncRNAs in multiple transcriptomes.

Homepage: Link

Publication Date: Jan. 18, 2021
Reference: [Journal] [Pubmed] [CrossRef]
Citations: 22 [via Pubmed]

Organism Specific:
  • plants
  • animals
  • mouse
  • fish
  • worm
  • rat
  • fly
  • human

    • Reference Genome Needed:
    Online/Local: /
    Installation/User Level: easy
    User Adjustability:
    User support:
    Precomputed Target Results Available For Download:
    Input Data Required:
  • FASTA files
  • FASTQ format
  • GSM/SRR sample IDs
  • accessible links to FASTA files

    • Cross-Refferences:
  • Phytozome
  • Ensembl
  • NONCODE
  • CANTATAdb 2.0
  • CIRCpedia v2.0
  • circAtlas 2.0
  • PlantcircBase
  • RNAcentral NAT
  • PlantNATsDB
  • piRBase
  • piRNAclusterDB
  • Pln24NT
  • miRBase
  • GtRNAdb
  • Rfam
  • Gene Ontology
  • Reactome
  • Disease Ontology
  • Network of Cancer Gene
  • DisGeNET disease genes
  • MSigDB
  • STRING PPI

    • Target Prediction
    Algorithm Features:
  • seed match
  • conservation
  • free energy
  • G:U pairs allowed in the seed

    • Target Region: 3'UTR,5'UTR,CDS,Any
    Target Annotation:
    Target Enrichment Analysis:
    NGS Data Needed:
    Metaserver:
    Target Prediction Methods Used For Metaserver:
  • miRanda
  • RNAhybrid

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

    • Sequencing Platform Specific:
    PARE/CLIP-Seq: /
    Differential Expression Analysis
    miRNA differential expression:
    mRNA differential expression:
    NGS Data Needed:
    Target Functional Analysis
    Analysis Features:
  • GO Terms
  • KEGG Pathways
  • Literature Mining
    • NGS Data Needed:
    Target Prediction Data Needed:
    Known miRNA Identification
    NGS Data Needed:
    IsomiRs Identification
    NGS Data Needed:





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