psRNATarget protocols

View psRNATarget computational protocol

psRNATarget statistics

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psRNATarget specifications

Information


Unique identifier OMICS_00414
Name psRNATarget
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Patrick Zhao <>

Additional information


http://plantgrn.noble.org/psRNATarget/help

Publications for psRNATarget

psRNATarget in pipelines

 (39)
2018
PMCID: 5759179
PMID: 29354114
DOI: 10.3389/fmicb.2017.02630

[…] (0.932) was applied to predicted mirna hairpins., micrornas function by providing a complementary sequence to parts of their target mrna. this can be predicted by diverse computational tools. here, psrnatarget (2011 release) (dai and zhao, ) was used to establish mirna—mrna interactions using default settings. while psrnatarget originally focused on plant mirna targeting, it now also includes […]

2018
PMCID: 5821703
PMID: 29467369
DOI: 10.1038/s41598-018-21560-1

[…] differentially expressed genes from all the combinations, i.e. (rc, rt), (lc, lt), (rc, lc) and (rt, lt) were considered for identification of tfs against planttfdb 3.0 with threshold e-value 1e-3., psrnatarget server was used for prediction of microrna targets against all the mature micrornas of poaceae family viz., aegilops tauschii, brachypodium distachyon, elaeis guineensis, festuca […]

2018
PMCID: 5838164
PMID: 29507325
DOI: 10.1038/s41598-018-22464-w

[…] to be significantly differential expression if they had p value ≤ 0.05 and log2 (fold change) ≥2., prediction of target genes of novel mirnas was performed against assembled rna-seq contigs using psrnatarget, with the default parameters and a maximum expectation value of 4 (number of mismatches allowed). function of each targeted gene was identified based on in-house sea buckthorn fruits […]

2018
PMCID: 5940787
PMID: 29739980
DOI: 10.1038/s41598-018-25315-w

[…] (srx751296). differential expression of smdml genes was analyzed using tophat2.0.12 and cufflinks2.2.1., s. miltiorrhiza small rnas potentially targeting smdmls for cleavage were predicted using psrnatarget. small rnas from roots, stems, leaves and flowers of s. miltiorrhiza were downloaded from sra database (srx686651, srx686652, srx686653 and srx686654). the maximum expectations of 3.0 […]

2017
PMCID: 5245829
PMID: 28103286
DOI: 10.1371/journal.pone.0168817

[…] 2 base 3’ overhangs expected for mirnas, and most of these were 22 nucleotides long (). we then tested if this group of potential mirna candidates had potential targets in the transcriptome using psrnatarget. using a stringent expect value of 0–2, psrnatarget identified 20 potential mirna sequences with predicted hits to a total of 53 different sequences in the transcriptome. however, none […]


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psRNATarget in publications

 (431)
PMCID: 5940787
PMID: 29739980
DOI: 10.1038/s41598-018-25315-w

[…] is targeted by nb_mirc1_3p. in order to know whether smdmls are regulated by mirnas, we searched high-throughput s. miltiorrhiza small rna database for mirnas potentially targeting smdmls using psrnatarget,. a total of 44 small rnas with sequence reads greater than four were identified under the maximum expectation of 3.0. the retrieved small rna sequences were aligned with s. miltiorrhiza […]

PMCID: 5945835
PMID: 29780401
DOI: 10.3389/fpls.2018.00608

[…] were determined using meme version 4.11.4 (bailey and elkan, ) (http://meme-suite.org/tools/meme) with the parameters as previous study (li and lu, ). mir156-targeted blspls were predicted using psrnatarget tool (http://plantgrn.noble.org/psrnatarget/; dai and zhao, )., putative cis-elements in the promoter regions (1,500 bp upstream sequences of the start codon) of blspls were annotated […]

PMCID: 5935748
PMID: 29728569
DOI: 10.1038/s41598-018-25349-0

[…] was used to create the sequence logo of the barley sbp domain. the genomic and cdna sequences of hvspls were analysed to predict the putative target sites of mir156 using psrnatarget tool (http://plantgrn.noble.org/psrnatarget/?function). information on alternative splice events for each hvspl gene was obtained from the ensemble database […]

PMCID: 5944317
PMID: 29774043
DOI: 10.3389/fpls.2018.00589

[…] aligned to the pokeweed mrna transcriptome and putative targets were identified using the plant small rna target analysis server with default parameters (dai and zhao, ; http://plantgrn.noble.org/psrnatarget/). this program predicts mirna/target pairs based on reverse complementary matching and target site accessibility, incorporating plant-specific features of target recognition., a paired […]

PMCID: 5916090
PMID: 29720988
DOI: 10.3389/fpls.2018.00499

[…] biological processes closely associate the mirna regulation on target genes at posttranscriptional or translation level. to define the target genes of taemir408, an online tool referred to as psrnatarget (plant microrna potential target finder) was adopted to predict the genes putatively interacted by taemir408. as suggested, the mature taemir408 sequence was subjected to scanning […]


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psRNATarget institution(s)
Bioinformatics and Computational Biology Lab, Noble Research Institute, Ardmore, OK, USA
psRNATarget funding source(s)
Supported by the National Science Foundation [DBI-0960897 and DBI1458597]; Noble Research Institute.

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