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miRProf specifications


Unique identifier OMICS_14630
Name miRProf
Alternative name miRNA Profiler
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Input data A set of sRNA samples and a genome file.
Input format A results table in .csv format and a list of sRNAs matching known miRNAs.
Output format CSV, FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Java
Computer skills Medium
Version 2.0
Stability No
Maintained No




No version available


This tool is not available anymore.

Publication for miRNA Profiler

miRProf citations


Roles of Non Coding RNA in Sugarcane Microbe Interaction

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

[…] t/rRNAs were removed. The remaining reads were then analyzed to identify novel and conserved miRNAs and siRNAs. The UEA sRNA toolkit—plant version was used to identify novel and conserved miRNAs. The miRProf pipeline was used to identify conserved miRNA. This approach matches sRNA libraries with known Viridiplantae mature and miRNA* deposited in miRBase database release 21 [], using the PatMaN pro […]


Small RNA and PARE sequencing in flower bud reveal the involvement of sRNAs in endodormancy release of Japanese pear (Pyrus pyrifolia 'Kosui')

BMC Genomics
PMCID: 4791883
PMID: 26976036
DOI: 10.1186/s12864-016-2514-8

[…] sRNA workbench, and ShortStack) to annotate miRNAs. miRProf uses similarity to search for matches while ShortStack and miRCAT identify miRNA sequences de novo. Utilizing annotations of known miRNAs, miRProf identified 137 miRNAs belonging to 32 known miRNA families, while ShortStack identified only 68 known miRNAs belonging to 22 families. Although BLAST-based strategies are more sensitive for id […]


Identification of miRNAs with potential roles in regulation of anther development and male sterility in 7B 1 male sterile tomato mutant

BMC Genomics
PMCID: 4625851
PMID: 26511108
DOI: 10.1186/s12864-015-2077-0
call_split See protocol

[…] nsposons, intron, CDs, and promoter regions were identified. Sequences were searched against rRNA, tRNA, snRNAs and snoRNAs from Rfam v.12 and NCBI nt/nr databases. Known miRNAs were identified using miRprof [], (available from the UEA sRNA workbench; http://srna-tools.cmp.uea.ac.uk/) allowing two mismatches with the mature miRNAs in miRBase database release 21 []. New miRNAs were predicted using […]


Genome wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize

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

[…] ze 28 nt. This tool matches sRNA libraries with known Viridiplantae mature miRNA deposited in miRBase database release 19 (http://www.mirbase.org/ftp.shtml), using a PatMaN program. The output of the miRProf showed sequences of miRNA that had at most one mismatch with the miRBase database and contained information about total and non-redundant sequence counts. To allow comparison between libraries […]


Small RNA Profile in Moso Bamboo Root and Leaf Obtained by High Definition Adapters

PLoS One
PMCID: 4117519
PMID: 25079776
DOI: 10.1371/journal.pone.0103590
call_split See protocol

[…] s in the sample, as indicated in . The differentially expressed reads were identified using offset fold change as described in , using an offset of 20. The miRNAs were identified using the miRCat and miRProf tools within the sRNA Workbench and custom made Perl scripts (Strawberry Perl v The miRNA targets were predicted using the target prediction tool within the UEA sRNA Workbench . Th […]


Differential sRNA Regulation in Leaves and Roots of Sugarcane under Water Depletion

PLoS One
PMCID: 3973653
PMID: 24695493
DOI: 10.1371/journal.pone.0093822

[…] Filtered sRNAs reads were submitted to the University of East Anglia sRNA toolkit-Plant version miRProf, which determines the expression levels of sRNAs matching them to known miRNAs at miRBase and at a specific genome. The expression level of a miRNA represents the number of occurrences of the […]


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miRProf institution(s)
School of Computing Sciences, University of East Anglia, Norwich, UK; School of Biological Sciences, University of East Anglia, Norwich, UK; The Sainsbury Laboratory, Norwich, UK
miRProf funding source(s)
This work was supported by the Biotechnology and Biological Sciences Research Council [grant number BB/E004091/1] and the Gatsby Charitable Foundation.

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