miRCat statistics

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Citations per year

Number of citations per year for the bioinformatics software tool miRCat

Tool usage distribution map

This map represents all the scientific publications referring to miRCat per scientific context
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Associated diseases

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miRCat specifications


Unique identifier OMICS_14629
Name miRCat
Alternative name miRNA Categorisation
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A file of sRNA sequences which are mapped to a plant genome using PatMaN and grouped into loci.
Input format FASTA
Output data A file with the details for predicted miRNA candidates, The RNAfold output for candidate precursors, A file of predicted mature miRNA sequences.
Output format PNG
Operating system Unix/Linux, Windows
Programming languages Java
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes


No version available


  • person_outline Vincent Moulton
  • person_outline Simon Moxon

Publication for miRNA Categorisation

miRCat citations


microRNAs associated with early neural crest development in Xenopus laevis

BMC Genomics
PMCID: 5774138
PMID: 29347911
DOI: 10.1186/s12864-018-4436-0

[…] for all reads aligning to miRNA hairpins in each sample. These counts were used as input for DESeq2_1.8.2. We considered padj < 0.01 to call differential expression. Novel miRNAs were predicted using miRCat and miRdeep2 [–]. The intersect was taken for prediction from both methods and the longest hairpin sequence obtained. The hairpin secondary structure was obtained using RNAFold []. Each hairpin […]


Roles of Non Coding RNA in Sugarcane Microbe Interaction

Noncoding RNA
PMCID: 5831913
PMID: 29657296
DOI: 10.3390/ncrna3040025

[…] erved miRNA. This approach matches sRNA libraries with known Viridiplantae mature and miRNA* deposited in miRBase database release 21 [], using the PatMaN program. Novel miRNAs were identified by the miRCat pipeline using sequences mapped to the available sugarcane sequence [] to find clusters of sRNA. Only new miRNA with 21 and 22 nt and that showed more than 25 reads were analyzed. In addition, […]


Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs

PMCID: 5545994
PMID: 28786034
DOI: 10.1186/s12284-017-0177-y

[…] allation, provides an user-friendly platform for sRNA-seq data processing (Stocks et al., ). It contains several useful tools, such as “adaptor remover” and “Filter” for sRNA-seq data pre-treatment, “miRCat” and “hairpin annotation” for miRNA prediction, and the ta-siRNA prediction tool. Besides, as noticed in Tables and , several valuable databases and bioinformatics tools, including Rice epigen […]


Integrative analysis of the Pekin duck (Anas anas) MicroRNAome during feather follicle development

BMC Dev Biol
PMCID: 5520360
PMID: 28728543
DOI: 10.1186/s12861-017-0153-1

[…] er miRBase (version 21.0). Reads that did not match any of the databases mentioned above were marked as non-annotated. Non-annotated sequences were searched against the Gallus gallus genome using the miRCat program included in the sRNAToolkit (http://srna-workbench.cmp.uea.ac.uk/tools/analysis-tools/mircat/). Using default settings, 100 nt flanking each side of the genomic sequences were extracted […]


Involvement of MicroRNAs in Probiotics Induced Reduction of the Cecal Inflammation by Salmonella Typhimurium

Front Immunol
PMCID: 5468434
PMID: 28659929
DOI: 10.3389/fimmu.2017.00704

[…] s perfectly matching known chicken miRNAs or precursors in the miRBase were considered as conserved mature miRNAs. Sequences that cannot match the sequences in the above database were analyzed by the miRCat program in the sRNA Toolkitsoft page () against the chicken genome. The genomic hit distribution patterns and secondary structure of genomic regions corresponding to sRNA hits were observed and […]


Profile and functional analysis of small RNAs derived from Aspergillus fumigatus infected with double stranded RNA mycoviruses

BMC Genomics
PMCID: 5450132
PMID: 28558690
DOI: 10.1186/s12864-017-3773-8
call_split See protocol

[…] was performed using three approaches; (i) similarity search against the miRBase database and known fungal miRNA-like entries, using a maximum of 3 mis-matches and no gaps (ii) miRNA prediction using miRCat [], (iii) additional analysis of expressed sRNAs, exclusion of those matching to existing annotations, and a search for a hairpin-like secondary structure by folding of the left and right flank […]

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miRCat institution(s)
The Earlham Institute, Norwich Research Park, Norwich, UK; School of Computing Sciences, Norwich, UK; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
miRCat funding source(s)
Supported by Biotechnology and Biological Sciences Research Council (BBSRC) (L021269/1).

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