TargetRNA protocols

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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 in pipelines

 (4)
2017
PMCID: 5511505
PMID: 28717590
DOI: 10.7717/peerj.3461

[…] 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 […]

2016
PMCID: 4809877
PMID: 27065955
DOI: 10.3389/fmicb.2016.00380

[…] regulate their antisense transcript efficiently (georg and hess, ) but this prediction represents the most likely target if an interaction is present. for trans-srnas, the target was predicted using targetrna2 (kery et al., ). the raw reads, bam mapping files, and count matrix data have been deposited in ebi's arrayexpress under accession number e-mtab-4468., dna probes to central regions […]

2016
PMCID: 5156373
PMID: 27973608
DOI: 10.1371/journal.ppat.1006084

[…] occurrence within each promoter of its respective promoter set., srna sequences were extracted from the a. actinomycetemcomitans 624 genome with the bedtools getfasta function [] and submitted to targetrna2 [] with default parameters and the a. actinomycetemcomitans strain d7s-1 genome selected. predicted target sequences in the d7s-1 genome were mapped in fasta format to the a. […]

2015
PMCID: 4683814
PMID: 26679185
DOI: 10.1186/s12864-015-2293-7

[…] 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 and coprarna, we have predicted the target mrnas regulated by r. prowazekii srnas. functional categorization of the target genes regulated by srnas resulted in identification of genes […]


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TargetRNA in publications

 (83)
PMCID: 5758910
PMID: 29069426
DOI: 10.1093/nar/gkx959

[…] regulator) genes. the size of the btsr1 was predicted to be 51 nt from the transcriptome data of ybt-1518. the transcription start site (+1) of btsr1 was determined by 5′-race (figure ). the targetrna program () gave a high score to a pairing between the btsr1 intergenic region and the 5′-utr of cry5ba mrna. a 13-bp sequence in btsr1 is complementary to the 5′-utr of the cry5ba mrna, […]

PMCID: 5581919
PMID: 28900423
DOI: 10.3389/fmicb.2017.01658

[…] to regulate their expression levels via perfect or limited base-pairing, the potential regulons of esre were screened with two comparative prediction algorithms for srna targets, coprarna () and targetrna (). twenty-four candidates were chosen for validation in vivo (supplementary table )., to further verify these candidates, translational fusions were generated by integrating the 5′ utrs […]

PMCID: 5586341
PMID: 28904860
DOI: 10.1002/2211-5463.12266

[…] pathway or biological role according to the kegg and uniprot databases , ., lc‐mse results, fold change, all genes p ≤ 0.01, boldfaced reached fdr control (bh) q ≤ 0.05., predicted in silico by targetrna, targetrna2 or coprarna , , ., to confirm the mass proteomic result that expression of petabc was repressed upon expression of nrrf, we assessed protein levels of cytochrome bc 1 […]

PMCID: 5542712
PMID: 28771593
DOI: 10.1371/journal.pone.0182582

[…] 72 hours. counts of dead worms were taken every 24 hours. a worm was considered dead if unresponsive to touch., sequence complementarity searches and alignments were performed using the blastn and targetrna2 servers [–]. the srba transcript sequence was queried limiting the searches to the ucbpp-pa14 genome. alignments returned were then manually checked to determine if the srba transcript […]

PMCID: 5493400
PMID: 28665976
DOI: 10.1371/journal.pone.0180386

[…] with unknown function, which makes the study of such putative target difficult to perform. therefore, we managed to identify direct targets of pesa rna by the use of the bioinformatics tool targetrna []. this tool predicted, as a high-scored output, an interaction in the region from -30 to -8 nt upstream the gene pyos3i of the pyos3 operon ( and ), predicted to encode pyocin s3 […]


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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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