TAPIR statistics

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TAPIR specifications


Unique identifier OMICS_04004
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for TAPIR

TAPIR in pipeline

PMCID: 5514137
PMID: 28717205
DOI: 10.1038/s41598-017-05085-7

[…] putative mirnas was set to 10. for each genotypes, mirna sequences identified were named based on the mirna family with the addition of the name of the genotype (2 c, a41, vs, vt, c3 and sp). the tapir standalone software was applied to identify the targets of the identified eggplant mirna on the predicted cdss. in particular, we applied the tapir hybrid function, which is based on the rna […]

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TAPIR in publications

PMCID: 5649071
PMID: 29052505
DOI: 10.1186/s12864-017-4209-1

[…] conserved and 13 novel mirnas differentially expressed during seed germination. of which, 43 conserved and nine novel mirnas showed distinct expression patterns between black and brown seed. using tapir, 208 unigenes were predicted as putative targets of 35 conserved mirna families and 17 novel mirna families. among functionally annotated targets, genes participated in transcription regulation […]

PMCID: 5662147
PMID: 28970560
DOI: 10.1038/s41477-017-0024-6

[…] sites are similar, we combined both types of target sites in the 8mer prediction, similar to guo et. al. 2010 and agarwal et. al. 2015,. target prediction based on the plant rule was performed via tapir., the list of mirna used was based on the 19 dcl3-dependent mirnas expressed based on the srna data, where the average reads within the complement is greater than 400 and the average ratio […]

PMCID: 5615367
PMID: 28925938
DOI: 10.3390/genes8090234

[…] viral or bacterial rna molecules., mirnaconstarget: consensus target prediction on user-provided input data based on miranda [], pita [] and targetspy [] for animal micrornas and psrobot [] and tapir (target prediction for plant micrornas) [] for plant micrornas., srnajbrowser: visualization of srna expression data in a genome context using jbrowse []., srnajbrowserde: visualization […]

PMCID: 5545994
PMID: 28786034
DOI: 10.1186/s12284-017-0177-y

[…] online tools for target prediction (table ), such as psrnatarget (a plant small rna target analysis server) (dai and zhao, ), small rna target prediction (jones-rhoades and bartel, ), and tapir (target prediction for plant micrornas) (bonnet et al., ). compared to tapir, the former two tools are more flexible for different users’ purposes. by using psrnatarget or small rna target […]

PMCID: 5517402
PMID: 28785273
DOI: 10.3389/fpls.2017.01278

[…] ., we used the following three target prediction methods with default parameters to predict the mirna targets: (i) psrna target tool using a score ≤4 for mrna and a score ≤4.5 for circrna (); (ii) tapir method () used a score ≤5 and ratio of the free energy of the duplex to the free energy of the same duplex having only perfect matches ≥0.7 for mrna and a score ≤6 and ratio of the free energy […]

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TAPIR institution(s)
Department of Plant Systems Biology, VIB, Gent, Belgium

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