PsRNA protocols

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PsRNA specifications

Information


Unique identifier OMICS_22244
Name PsRNA
Software type Application/Script
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained No

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This tool is not available anymore.

Publication for PsRNA

PsRNA in pipelines

 (3)
2017
PMCID: 5590963
PMID: 28886174
DOI: 10.1371/journal.pone.0184528

[…] targets of srnas action with default parameters: 1) the uea srna toolkit [], which was used as a standalone application (version may 18, 2012) and 2) the plant small rna target analysis server (psrna target) [], which was used as a www application available at: http://plantgrn.noble.org/psrnatarget/., in the selection of targets for rt-qpcr analysis, we focused on four different groups […]

2015
PMCID: 4570225
PMID: 26369665
DOI: 10.1186/s12864-015-1851-3

[…] an error bar. all the primers used are listed in table .table 3, target prediction for drought-responsive mirnas and novel mirna candidates against indica rice 9311 fgenesh genes was conducted using psrna target: a plant small rna target analysis server [] using default setting except the maximum expectation. this is the score of complementarity between mirna and its target, which was adjusted […]

2014
PMCID: 3954700
PMID: 24633051
DOI: 10.1371/journal.pone.0091369

[…] phylogenetic tree analysis and reliability values at each branch representing bootstrap samples (1000 replicates). prediction of mature mir169 family member targets was performed online with the psrna server using relatively strict rules (http://plantgrn.noble.org/psrnatarget/), including a maximum expectation value of 3.5, a length for complementarity scoring (hsp size) of 21 bp, a target […]


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PsRNA in publications

 (79)
PMCID: 5811567
PMID: 29440670
DOI: 10.1038/s41598-018-21193-4

[…] in diverse biological processes by cleaving target mrnas or suppressing the translation of target genes. in order to understand the biological functions of l. lancifolium mirnas, targetfinder and psrna target software was used to predict putative target genes of novel and conserved mirnas. the results from analysis showed that 366 target genes for 17 conserved mirna families and 415 target […]

PMCID: 5831913
PMID: 29657296
DOI: 10.3390/ncrna3040025

[…] the expression levels were normalized to compare the expression in all libraries. interestingly, two novel mirnas had both mature mirna and mirna* identified in the same library (; a,b). using a psrna target, it was possible to identify putative targets for 84 novel mirnas in sugarcane (). in this analysis, the expressed sequence tags (est) sugarcane data from gene index version 3.0 was used […]

PMCID: 5702422
PMID: 29209340
DOI: 10.3389/fpls.2017.01943

[…] (vi) the predicted secondary structure must contain high negative mfe and high mfei values., in order to understand the biological functions of mirnas, putative target genes were identified by using psrna target server (http://plantgrn.noble.org/psrnatarget/) against available b. juncea transcript sequences and b. rapa unigenes, which is close to juncea (as it contains aa genome) (mun et al., ). […]

PMCID: 5668248
PMID: 29097749
DOI: 10.1038/s41598-017-14973-x

[…] other arm, 5) no loop or break in mirna sequences,and 6) predicted secondary structures should have high negative minimum fold energies (less than or equal to −20 kcal/mol)., the plant small rna (psrna) target (http://plantgrn.noble.org/psrnatarget/) analysis server was used to predict mrna targets corresponding to identified mirnas based on customised parameters. prediction analysis […]

PMCID: 5668977
PMID: 29096602
DOI: 10.1186/s12864-017-4238-9

[…] known and novel mirnas were identified (additional file : table s8 and table s9). a total of 545 unique target genes of 38 known and 39 novel differentially expressed mirnas were predicted using the psrna target server []. interestingly, each mirna family had multiple predicted targets that were functionally divergent. analysis of these predicted targets showed that approximately 10% of mirna […]


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PsRNA institution(s)
Centre of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University, Madurai, India; Bioinformatics Centre, Indian Institute of Science, Bangalore, India; Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India
PsRNA funding source(s)
Supported by the Department of Biotechnology (DBT), Government of India.

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