RotaC protocols

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RotaC specifications

Information


Unique identifier OMICS_22641
Name RotaC
Interface Web user interface
Restrictions to use Academic or non-commercial use
Programming languages Java, Perl, PHP
Computer skills Basic
Version 1.0
Maintained Yes

Maintainers


  • person_outline Piet Maes <>
  • person_outline Jelle Matthijnssens <>
  • person_outline Mustafizur Rahman <>
  • person_outline Marc Van Ranst <>

Publication for RotaC

RotaC in pipelines

 (17)
2018
PMCID: 5774894
PMID: 29142125
DOI: 10.1128/JVI.01246-17

[…] strains by using both de novo and reference dna sequence assembler algorithms implemented in geneious software v8 (). rotavirus genotypes were assigned to each of the 11 genome segments by using the rotac v2.0 web-based automated rotavirus genotyping tool (http://rotac.regatools.be/) ()., reference nucleotide sequences for each rotavirus genome segment were retrieved from the rotavirus resource […]

2017
PMCID: 5214804
PMID: 28070453
DOI: 10.7717/peerj.2733

[…] further analysis and deposited in genbank under accession numbers: kx954616– kx954624., the genotypes for each of the eleven gene segments were determined using the online rotavirus genotyping tool, rotac (http://rotac.regatools.be) (). sequences were aligned and the most optimal nucleotide substitution model was determined in mega 5 (). maximum likelihood phylogenetic tree construction […]

2017
PMCID: 5597190
PMID: 28902863
DOI: 10.1371/journal.pone.0184067

[…] and virustap []. contigs derived from either rotavirus wild-type strains or rotarix strain were identified by blast search. genotypes of each contigs were determined by an automated genotyping tool rotac 2.0 (http://rotac.regatools.be/) according to the guideline proposed by rcwg., the representative gene sequences of rva strains obtained in this study were deposited into genbank […]

2017
PMCID: 5702219
PMID: 29178883
DOI: 10.1186/s12917-017-1280-4

[…] 2.9 (roche). the geneious software suite v 9.0.5 (biomatters ltd, auckland, new zeland) was used for visualization and final data analysis. to obtain the genomic constellation of the rva strain, the rotac v 2.0 online automated genotyping tool [] was used to assign the genotype of each genome segment., selected sequences of rva deposited in genbank, with complete genome and genotype relevant […]

2016
PMCID: 4742054
PMID: 26845439
DOI: 10.1371/journal.pone.0148416

[…] using genetyx v11 (genetyx)., the genotype of each of the 11 gene segments of strains skt-281, skt-289, ls-04, pcb-118, skt-98, bd-20, np-m51, skt-138, and sskt-133 was determined using the rotac v2.0 automated genotyping tool (http://rotac.regatools.be/) [] according to the guidelines proposed by the rotavirus classification working group (rcwg)., sequence comparisons were carried […]


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RotaC in publications

 (41)
PMCID: 5964442
DOI: 10.1128/mSystems.00025-18

[…] number of rotavirus types present in this sample. given the amino acid similarities with both rva and rvc types, we suggest there are at least two and possibly three types present here., using the rotac 2.0 typing tool for rva and blast-based similarity to known genotypes, we have typed the rotavirus genome segments found here (). the combined genomic makeup of the rv community in sample […]

PMCID: 5905509
DOI: 10.1093/ve/vey010.046

[…] and six animal (one bovine, one caprine, and four porcine) rva strains identified in uganda in the same geographical region, between 2012 and 2014 was undertaken using the illumina hiseq platform. rotac version 2, a classification tool for rvas was used to assign genotypes to all eleven genome segments of each isolate. phylogenetic analysis was carried out using the maximum likelihood method […]

PMCID: 5799398
PMID: 28057906
DOI: 10.4142/jvs.2018.19.1.35

[…] correlations to diarrhea-inducing capabilities and evolution of nsp4 in the porcine population. full-length nsp4 genes were amplified, cloned, sequenced, and then analyzed for antigenic epitopes, rotac classification, homology, genetic relationship, modeling of nsp4 protein, and prediction of post-translational modification. rv presence was observed in both diarrheic and non-diarrheic […]

PMCID: 5772666
PMID: 29343800
DOI: 10.1038/s41598-018-19469-w

[…] from samples with the highest viral loads were amplified and sequenced. all primers used are listed in supplementary table . virus genotype and nucleotide sequence similarities were analysed by the rotac v2.0 (http://rotac.regatools.be/) automated genotyping tool and blastn (http://www.ncbi.nlm.nih.gov/)., five samples were also culture-adapted to ma104 cells as previously described […]

PMCID: 5774894
PMID: 29142125
DOI: 10.1128/JVI.01246-17

[…] strains by using both de novo and reference dna sequence assembler algorithms implemented in geneious software v8 (). rotavirus genotypes were assigned to each of the 11 genome segments by using the rotac v2.0 web-based automated rotavirus genotyping tool (http://rotac.regatools.be/) ()., reference nucleotide sequences for each rotavirus genome segment were retrieved from the rotavirus resource […]


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RotaC institution(s)
Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
RotaC funding source(s)
Supported by a postdoctoral grant from the 'Fonds voor Wetenschappelijk Onderzoek (FWO)-Vlaanderen'; by the Institute for the Promotion and Innovation through Science and Technology in Flanders (IWT Vlaanderen).

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