miRCat protocols

View miRCat computational protocol

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miRCat specifications

Information


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

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Maintainers


  • person_outline Vincent Moulton <>
  • person_outline Simon Moxon <>

Publication for miRNA Categorisation

miRCat in pipelines

 (3)
2016
PMCID: 4989143
PMID: 27535581
DOI: 10.1038/srep31766

[…] bank (http://pirnabank.ibab.ac.in/). the maximum number of mismatches allowed was two bases, and a two-base shortening or extension at both ends of the sequence was allowed during the alignment. the mircat tool in the srna tool kit was used to predict novel mirnas. the remaining non-annotated srna sequences were aligned against the chicken genome sequence, and genomic sequences containing […]

2015
PMCID: 4465036
PMID: 26061962
DOI: 10.1371/journal.pone.0129738

[…] 5.5., novel mirnas discovery: the unannotated small rna sequences were aligned to the reference chicken (g.gallus) genome to find precursor sequences for novel mirnas. novel mirnas were predicted by mircat tools with stem-loop structure., differentially expressed mirnas analysis: the r package degseq software was used to identify differentially expressed mirnas. the number of conserved mirnas […]

2014
PMCID: 4168055
PMID: 25194793
DOI: 10.1186/1471-2164-15-766

[…] analysis (fisher exact test) was performed with a p-value cutoff < 0.05 and bonferroni correction., novel mirnas were identified in the maize libraries using the uea srna toolkit (plant version) mircat pipeline. sequences were mapped to the maize genome (b73 refgen_v2) to find clusters of srna. the most abundant srna read within a cluster was chosen as the likely mirna candidate. only new […]


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miRCat in publications

 (90)
PMCID: 5774138
PMID: 29347911
DOI: 10.1186/s12864-018-4436-0

[…] 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 []. […]

PMCID: 5744193
PMID: 29312421
DOI: 10.3389/fpls.2017.02192

[…] mirna (meyers et al., ). mirnas that had different 5′ and 3′ ends with respect to the mature mirna, were annotated as isomirs. to identify novel unannotated mirnas, filtered reads were submitted to mircat tool of the uea srna toolkit using default parameters for plants, considering only reads of lengths 18–24 nt. reads were first mapped to the potato genome, then the 100 and 200 nt long windows […]

PMCID: 5831913
PMID: 29657296
DOI: 10.3390/ncrna3040025

[…] against the sugarcane genome sequencing by methylation filtration database [] identified additional 131 new sugarcane mirnas, 21 and 22 nt in length, from mock and infected libraries using the mircat pipeline (). the mfei (minimum fold free energy index), another parameter used to evaluate the novel mirna precursors, was calculated manually according to zhang et al. (2006) []. […]

PMCID: 5731802
PMID: 28805496
DOI: 10.1080/15476286.2017.1356564

[…] used for small rnas cloning, northern blot analysis and cell transfection., small rnas derived from dicer digestion of nat6531 were purified by mirvana™ mirna isolation kit (ambion) and cloned using mircat small rna cloning kit (integrated dna technologies) according to the manufacturer's protocol. a total of 18 clones were sequenced., dicer digestion products of in vitro transcribed nat6531 […]

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

[…] 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 […]


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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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