NetPicoRNA protocols

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NetPicoRNA specifications

Information


Unique identifier OMICS_02446
Name NetPicoRNA
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Nikolaj Blom <>

Publication for NetPicoRNA

NetPicoRNA in pipelines

 (3)
2017
PMCID: 5240211
PMID: 28095784
DOI: 10.1186/s12866-016-0923-0

[…] generated by de novo assembly algorithm were analyzed using blastn., hypothetical polyprotein cleavage sites of the viruses were predicted by multiple alignments with other bevs and confirmed by the netpicorna []. nucleotide (nt) sequences or amino acid (aa) sequences were aligned using clustalw. phylogenetic trees were constructed by maximum likelihood (ml) methods on mega5.2.2 []. the mtrev24 + […]

2015
PMCID: 4603672
PMID: 26461027
DOI: 10.1371/journal.pone.0139668

[…] each fragment, at least three clones (if conflict occurs, up to eight clones) were sequenced to determine the consensus sequence of any given region., the obtained genome sequence was submitted to netpicorna 1.0 server [] and also aligned with the available polyproteins of chpv1 100c (kf979332) [] and sicinivirus 1 strain ucc001 (nc_023861) [] to predict possible polyprotein cleavage sites. […]

2014
PMCID: 3931614
PMID: 24586283
DOI: 10.1371/journal.pone.0087593

[…] of structural and non-structural proteins were done based on amino acid alignments with reference picornavirus sequences from genbank and the presence of cleavage sites identified using the netpicorna program . cleavage sites at the interdomain junctions were predicted based on the preference of picornaviruses for glutamine (q) and glutamic acid (e) at the p1 position of the cleavage […]


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NetPicoRNA in publications

 (19)
PMCID: 5839581
PMID: 29509804
DOI: 10.1371/journal.pone.0193881

[…] 0.123 offset value) and selecting conserved domains with similarity to other nyamiviridae []. additionally, putative protease cleavage sites of pcn picorna-like virus (plv) were predicted via the netpicorna 1.0 server (http://www.cbs.dtu.dk/services/netpicorna/) []., a read information represents three pooled biological replicates., b sequence data spans the length of the genome; however, […]

PMCID: 5793394
PMID: 29386036
DOI: 10.1186/s12929-018-0412-x

[…] role in viral protein stability.fig. 2fig. 3, we proposed a scenario in which p90atf6 is beneficial for viral replication, but it undergoes cleavage to generate p45atf6. a prediction algorithm (netpicorna 1.0) revealed several potential picornaviral protease cleavage sites in atf6; thus, we examined the possibility of cleavage by the ev-a71-encoded proteases 2apro and 3cpro. plasmids […]

PMCID: 5738146
PMID: 29220410
DOI: 10.1371/journal.ppat.1006744

[…] negative mutant of nfat5 [, ], implying the potential influence of p70-nfat5 on overall nfat5 activity. therefore, we focused our study on p70-nfat5, the 2a cleavage product. we utilized the program netpicorna 1.0 [] to analyze the whole aa sequence of nfat5 and predicted the peptide bond just before g503 as the top candidate site of 2a cleavage (). interestingly, the predicted 2a recognition […]

PMCID: 5656790
PMID: 28590234
DOI: 10.1099/jgv.0.000799

[…] (ealfq*gppt) []. to investigate the insertion of the plpro in the texas ev-g stains, a cleavage site analysis was performed by submitting the full-length orf of the texas ev-g strains to the netpicorna 1.0 server [], which predicted two highly probable cleavage sites (0.958/1.0 cleavage scores) flanking the insertion region (. thus, this analysis suggests that the plpro insertion […]

PMCID: 5240211
PMID: 28095784
DOI: 10.1186/s12866-016-0923-0

[…] generated by de novo assembly algorithm were analyzed using blastn., hypothetical polyprotein cleavage sites of the viruses were predicted by multiple alignments with other bevs and confirmed by the netpicorna []. nucleotide (nt) sequences or amino acid (aa) sequences were aligned using clustalw. phylogenetic trees were constructed by maximum likelihood (ml) methods on mega5.2.2 []. the mtrev24 + […]


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NetPicoRNA institution(s)
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

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