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PAREsnip specifications

Information


Unique identifier OMICS_05983
Name PAREsnip
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Vincent Moulton

Publication for PAREsnip

PAREsnip citations

 (21)
library_books

Transcriptome analysis reveals new microRNAs mediated pathway involved in anther development in male sterile wheat

2018
BMC Genomics
PMCID: 5941544
PMID: 29739311
DOI: 10.1186/s12864-018-4727-5

[…] and antisense tags. The tags mapped to cDNA or mRNA sequences were then used to predict cleavage sites. The pure reads with 20 and 21 nucleotides were used to identify potentially cleaved targets by PAREsnip (http://srna-workbench.cmp.uea.ac.uk/tools/paresnip/) and CleaveLand 3.0 (http://sites.psu.edu/axtell). The targets predicted were classified into five categories (0, 1, 2, 3 and 4) according […]

library_books

High throughput deep degradome sequencing reveals microRNAs and their targets in response to drought stress in mulberry (Morus alba)

2017
PLoS One
PMCID: 5325578
PMID: 28235056
DOI: 10.1371/journal.pone.0172883

[…] of the sequence was a single base. Next, distinct tags that perfectly matched mulberry cDNA or mRNA sequences by SOAP2.20 based on Genbank of NCBI (http://www.ncbi.nlm.nih.gov/), the known miRNAs by PAREsnip from miRBase (miRBase21.0: http://www.mirbase.org/), or miRNAs identified in other studies [,] were used to analyze miRNA-mRNA pairs. Alignments were then scored according to a previously des […]

library_books

tRNA derived small RNAs target transposable element transcripts

2017
Nucleic Acids Res
PMCID: 5605234
PMID: 28335016
DOI: 10.1093/nar/gkx103

[…] sing PatMaN through the UEA sRNA workbench (). Predictions of tRF target genes were made using the psRNA-Target () using a mRNA/tRF pair scoring cutoff of E ≤ 5. PARE-seq libraries were analyzed with PAREsnip through the UEA sRNA workbench (). The default high stringency settings were used, removing the t/rRNA filtering step. Protein coding genes and TEs identified through this method were further […]

library_books

Small RNAs Derived from the T DNA of Agrobacterium rhizogenes in Hairy Roots of Phaseolus vulgaris

2017
Front Plant Sci
PMCID: 5285386
PMID: 28203245
DOI: 10.3389/fpls.2017.00096

[…] o AGO protein-complexes. Most of them could be loaded onto AGO1, which has an important role in antiviral silencing (Peláez and Sanchez, ). The interactions detected for conserved microRNAs using the PAREsnip algorithm and the degradome data were mainly validated interactions. For this reason, the amount of interactions detected between ArT-sRNAs and host transcripts suggests that ArT-sRNAs may he […]

library_books

Small RNA mediated responses to low and high temperature stresses in cotton

2016
Sci Rep
PMCID: 5067717
PMID: 27752116
DOI: 10.1038/srep35558

[…] mismatches allowed on the 10th and 11th nucleotides of mature miRNAs where the splice site on miRNA targets generally occurs in degradome analysis. Potential miRNA targets with a P-value of < 0.05 by PAREsnip software were retained, and T-plot figures were drawn. All target sequences were categorized into five classes based on the abundance of degradome tags indicating miRNA-mediated cleavage. The […]

library_books

Comparative Analysis of miRNAs and Their Target Transcripts between a Spontaneous Late Ripening Sweet Orange Mutant and Its Wild Type Using Small RNA and Degradome Sequencing

2016
Front Plant Sci
PMCID: 5030777
PMID: 27708662
DOI: 10.3389/fpls.2016.01416

[…] g unannotated sequences were mapped to the reference genes (cDNA) of the C. sinensis genome (Xu et al., ) by SOAP2 (Li et al., ). The reads mapped to cDNA_sense were used to predict cleavage sites by PAREsnip (version 2.3; Folkes et al., ). The cleaved target transcripts were categorized into five classes based on the abundance of degradome reads indicative of miRNA-mediated cleavage. Category 0 c […]

Citations

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PAREsnip institution(s)
School of Computing Sciences, University of East Anglia, Norwich, UK; School of Biological Sciences, University of East Anglia, Norwich, UK
PAREsnip funding source(s)
Supported by Biotechnology and Biological Sciences Research Council [BB/L021269/1] and the BBSRC NRP DTP.

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