TargetRNA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool TargetRNA
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Tool usage distribution map

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

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Popular tool citations

chevron_left Bacterial sRNA target prediction chevron_right
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Protocols

TargetRNA specifications

Information


Unique identifier OMICS_03818
Name TargetRNA
Interface Web user interface
Restrictions to use None
Input data TargetRNA2 takes the sequence of a sRNA and the name of a sequenced bacterial replicon.
Output data It outputs a ranked list of likely regulatory targets for the input sRNA.
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Brian Tjaden

Publications for TargetRNA

TargetRNA citations

 (26)
library_books

Identification and validation of sRNAs in Edwardsiella tarda S08

2017
PLoS One
PMCID: 5340389
PMID: 28267754
DOI: 10.1371/journal.pone.0172783

[…] f sRNAs in all bacterial lineages, little is known about their function and mechanism of action within the bacterial genomes and only a few sRNAs have been assigned with functions till date []. Using TargetRNA2, we have predicted the target mRNAs of 10 sRNAs.Functional categorization of the target genes regulated by sRNAs resulted in identification of genes involved in key pathways of cell divisio […]

library_books

Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions

2017
Nucleic Acids Res
PMCID: 5435917
PMID: 28334800
DOI: 10.1093/nar/gkx115

[…] hese approaches have been followed by several methods that display varying degrees of accuracy and sophistication: from (i) those neglecting intramolecular structure (e.g. RNAduplex (), RNAhybrid (), TargetRNA () and RNAplex ()) to (ii) those considering only one interaction site and intramolecular structure (e.g. Nupack (), RNAup (), AccessFold () and IntaRNA ()), or even to (iii) those highly co […]

library_books

Construction of a fur null mutant and RNA sequencing provide deeper global understanding of the Aliivibrio salmonicida Fur regulon

2017
PeerJ
PMCID: 5511505
PMID: 28717590
DOI: 10.7717/peerj.3461

[…] of their presence in bacterial genomes although their significance is not fully understood (). Finally, EDGE-pro and DESeq was used to estimate differential gene expression levels for the sRNAs/sORFs.TargetRNA2 and IntaRNA were used to identify potential sRNAs targets (; ). Using sRNA sequences as queries, the programs searches for complementary regions in 5′ regions of mRNAs. Only targets predict […]

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

[…] the RNA–RNA interaction prediction tools (; ; ). Many secondary structure prediction tools also utilize MFE methods (; ; ; ). Some MFE methods including RNAhybrid (), RNAduplex (), DuplexFold () and TargetRNA () neglect intramolecular structures for the sake of algorithmic speed. Algorithms like Pairfold (), RNAcofold () and bifold () take intramolecular base-pairing into account. RNAup (), RNApl […]

library_books

Small Regulatory RNAs of Rickettsia conorii

2016
Sci Rep
PMCID: 5105140
PMID: 27834404
DOI: 10.1038/srep36728

[…] ecretory systems in R. conorii. An important consideration in this context, however, is that approximately 44% of top predictions by CopraRNA turn out to be true and the success rates for IntaRNA and TargetRNA as target prediction tools are 28 and 11%, respectively. Experimental verification and repudiation of R. conorii genes predicted as potential targets of Rc_sRs by such algorithms would, ther […]

library_books

Identification and Characterization of Novel Small RNAs in Rickettsia prowazekii

2016
Front Microbiol
PMCID: 4896933
PMID: 27375581
DOI: 10.3389/fmicb.2016.00859

[…] NA. We have further performed RLM-RACE to identify their transcription start sites and computational promoter analysis on the confirmed sRNAs. Also, target predictions using two independent programs, TargetRNA2 and IntaRNA, have revealed probable mRNA targets for each trans-acting sRNA.Most sRNAs described to date have been found in model organisms, such as Escherichia coli, Salmonella enterica se […]


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TargetRNA institution(s)
Computer Science Department, Wellesley College, Wellesley, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
TargetRNA funding source(s)
This work was supported by the National Institutes of Health [U19 AI107774, R15 GM102755].

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