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RNASnoop specifications

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Unique identifier OMICS_23836
Name RNASnoop
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Hakim Tafer

Publication for RNASnoop

RNASnoop citations

 (8)
library_books

PlantRNA_Sniffer: A SVM Based Workflow to Predict Long Intergenic Non Coding RNAs in Plants

2017
Noncoding RNA
PMCID: 5831995
PMID: 29657283
DOI: 10.3390/ncrna3010011

[…] large datasets, CPC works well with known protein coding transcripts, but may tend to classify novel PCTs into ncRNAs, if they have not been recorded in the protein databases. PSoL [], SnoReport [], RNAsnoop [], and SnoStrip [] are methods designed to classify small ncRNAs. LncRScan-SVM [], lncRNA-MFDL [], lncRNA-ID [], lncRNApred [], PLEK [], and CNCI [] are methods that use machine learning tec […]

library_books

A comprehensive benchmark of RNA–RNA interaction prediction tools for all domains of life

2016
Bioinformatics
PMCID: 5408919
PMID: 27993777
DOI: 10.1093/bioinformatics/btw728

[…] ct interactionsSome RNA–RNA interaction prediction tools are developed to achieve a specific task or to predict very specific group of interactions. For example, PLEXY is designed for C/D snoRNAs (), RNAsnoop () for H/ACA snoRNAs and TargetRNA () for bacterial sRNAs (E. coli and Salmonella). In this study, we tried to assess the versatility of prediction tools on different datasets as well as thei […]

library_books

An updated human snoRNAome

2016
Nucleic Acids Res
PMCID: 4914119
PMID: 27174936
DOI: 10.1093/nar/gkw386

[…] a recent high throughput study () for pseudouridine sites and from the newly developed RimSeq method for 2′-O-methylation sites.At first, we predicted putative targets on human rRNAs and snRNAs using RNAsnoop () and Plexy () for human H/ACA box and human C/D box snoRNAs, respectively. Precomputed RNAup structure profiles of target RNAs () were provided to refine interaction predictions with RNAsno […]

library_books

Promoter based identification of novel non coding RNAs reveals the presence of dicistronic snoRNA miRNA genes in Arabidopsis thaliana

2015
BMC Genomics
PMCID: 4660826
PMID: 26607788
DOI: 10.1186/s12864-015-2221-x

[…] losely related species and lack of homologs in distant ones may indicate the recent origin of the identified novel snoRNA genes.Targets for C/D and H/ACA snoRNAs were predicted using the PLEXY [] and RNAsnoop [] programs, respectively. Seven snoRNAs were shown to target the methylation of 18S or 25S rRNA-specific residues (Table ). In addition, 13 other predicted C/D box snoRNAs were found to targ […]

library_books

Revisiting the structure/function relationships of H/ACA( like) RNAs: a unified model for Euryarchaea and Crenarchaea

2015
Nucleic Acids Res
PMCID: 4652768
PMID: 26240384
DOI: 10.1093/nar/gkv756

[…] alignments using the R2R program (). The structure representations of the guide:target RNA pairs are also generated using the R2R program. The corresponding pairing energies are calculated using the RNAsnoop utility () from the Vienna Package (version 2.0) (). In the analysis of the energy contributions to the duplex stability, we refer to the 5’ and 3’ duplex as defined in RNAsnoop.In the case o […]

library_books

Unusual Novel SnoRNA Like RNAs in Drosophila melanogaster

2015
Noncoding RNA
PMCID: 5932544
DOI: 10.3390/ncrna1020139

[…] atively classified as scaRNAs. In particular, MeU1:95C-A24 is predicted to recognize all D. melanogaster U1 snRNA isoforms, see also .Targets for the orphan snoRNAs were then sought genome-wide using RNAsnoop and PLEXY with default parameters. No plausible target site was found for any of the box H/ACA snoRNAs. This may be explained by their reduced sequence length, which impedes the formation of […]


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RNASnoop institution(s)
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria; Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany; Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany; RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Leipzig, Germany; The Santa Fe Institute, Santa Fe, NM, USA
RNASnoop funding source(s)
Supported by European Union under the auspices of the FP-6 SYNLET and the FP-7 QUANTOMICS project and the Austrian GENAU project ‘Regulatory Noncoding RNA’.

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