PsRobot protocols

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PsRobot specifications

Information


Unique identifier OMICS_04009
Name PsRobot
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PsRobot

PsRobot in pipelines

 (9)
2018
PMCID: 5908857
PMID: 29674749
DOI: 10.1038/s41598-018-24477-x

[…] with c. songorica transcriptome data (prjna356791). novel mirna precursors were also predicted using the same data set., the potential target genes of c. songorica mirna were predicted using psrobot (http://omicslab.genetics.ac.cn/psrobot/), and those predicted target genes were employed to annotate functions and pathways. numerous target sequences were assigned to go enrichment and kegg […]

2018
PMCID: 5946474
PMID: 29747577
DOI: 10.1186/s12864-018-4754-2

[…] and then analyzed their function. fragments per kilobase for a million reads (fpkms) of both lncrnas and coding genes in each sample [] were calculated by the cuffdiff (v2.1.1). unlike the former, psrobot [] was used to predict the mirna binding sites of circrnas. besides, the transcript per million (tpm) was used to normalize the expression level of circrnas according to the criteria […]

2017
PMCID: 5366869
PMID: 28345652
DOI: 10.1038/srep45132

[…] reads were extracted and mapped to the bryv or pemv 2 genomes by bowtie. only the small rnas showed perfect matches to the sense or antisense viral genomic sequences were identified as vsirnas., the psrobot program was used to predict plant transcripts targeted by vsirnas generated from bryv and pemv 2 in co-infected n. benthamiana plants. the go analysis was conducted to annotate the predicted […]

2017
PMCID: 5447065
PMID: 28611800
DOI: 10.3389/fpls.2017.00873

[…] mirnas with false discovery ration (fdr) < 0.05 were defined as de-mirnas., novel mirna were first predicted by mirplant v5 with cut off score over 0. their secondary structures were predicted by psrobot with the criteria of having large stem loop; mismatches in small rna region between 0 and 7, and maximal precursor length of 200 nt (wu et al., ; an et al., ). then these candidates […]

2017
PMCID: 5447065
PMID: 28611800
DOI: 10.3389/fpls.2017.00873

[…] secondary structures predicted by psrobot (wu et al., ), mfold (http://mfold.rna.albany.edu/?q= mfold), and mirplant v5 were selected as final candidates., mirna targets were also predicted by psrobot (wu et al., ). our criteria included: (1) penalty score threshold = 2 (the penalty score of each candidate alignment is obtained by subtracting the actual alignment score from the ideal […]


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PsRobot in publications

 (65)
PMCID: 5946474
PMID: 29747577
DOI: 10.1186/s12864-018-4754-2

[…] and then analyzed their function. fragments per kilobase for a million reads (fpkms) of both lncrnas and coding genes in each sample [] were calculated by the cuffdiff (v2.1.1). unlike the former, psrobot [] was used to predict the mirna binding sites of circrnas. besides, the transcript per million (tpm) was used to normalize the expression level of circrnas according to the criteria […]

PMCID: 5941544
PMID: 29739311
DOI: 10.1186/s12864-018-4727-5

[…] database for family classification; novel mirnas precursor was submitted to rfam (http://xfam.org/) to search rfam families. target genes of known and novel mirna were predicted using psrobot software., for the degradome sequencing, equal amounts of all nn (nn1–1, nn1–2, nn2–1 and nn2–2) or sl (sl1–1, sl1–2, sl2–1 and sl2–2) rna samples used in small rna sequencing were mixed […]

PMCID: 5932338
PMID: 29755439
DOI: 10.3389/fmicb.2018.00818

[…] were used for novel mirna prediction by using mireap (). the raw abundance of milrnas was normalized according to transcripts per million (tpm) normalization, where the n_base is 1,000,000 (; ). psrobot () and targetfinder () were used for the prediction of mirna according to plant-like target interactions, and based on the methods described by allen with slightly modified: (1) less […]

PMCID: 5937831
PMID: 29690862
DOI: 10.1186/s12864-018-4678-x

[…] of the mirnas responsive to high-temperature stress and exogenous spd, we compared the mirna sequences to the est sequences of the cucumber genome. the bioinformatics software target finder [] and psrobot [] was used to predict genes targeted by mirnas involved in the response to both high temperature and exogenous spd, taking the intersection as the predicted result. the intersections […]

PMCID: 5908857
PMID: 29674749
DOI: 10.1038/s41598-018-24477-x

[…] mirnas only expressed in cl_b). the differential expression of 124 novel mirnas was showed in fig.  (table ).figure 4figure 5, the potential target genes of c. songorica mirna were predicted by psrobot. 1,657, 1,776, 1,868 and 1,407 potential target genes were identified and were corresponding to 78 mirnas in ch flowers, 73 mirnas in cl_b flowers, 99 mirnas in cl_m, and to 90 mirnas […]


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PsRobot institution(s)
The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

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