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Protocols

G2P specifications

Information


Unique identifier OMICS_19709
Name G2P
Alternative name Gene2Phenotype
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline G2P Team

Additional information


https://github.com/at7/ensembl-gene2phenotype https://github.com/at7/gene2phenotype_app

Publications for Gene2Phenotype

G2P citations

 (48)
call_split

Emergence of Human G2P[4] Rotaviruses in the Post vaccination Era in South South Korea: Footprints of Multiple Interspecies Re assortment Events

2018
Sci Rep
PMCID: 5902508
PMID: 29662148
DOI: 10.1038/s41598-018-24511-y
call_split See protocol

[…] The nucleotide sequences of the G2P[4] strains were compared with representative rotavirus sequences available in the GenBank database. Phylogenetic trees were constructed using the neighbour joining algorithm in PHYLIP and the Kimu […]

library_books

Distribution of Rotavirus Genotypes Circulating in Ahvaz, Iran in 2016

2018
PMCID: 5786656
PMID: 28915725
DOI: 10.22034/ibj.22.2.107

[…] us genotypes. A considerable amount of non-typeable genotypes has been reported in studies for G (20.2%; range 5%-41%) and P (17%; range 1.4%-28.2%) genotypes[]. The most prevalent genotypes, G1P[8], G2P[4], G3P[8], G4P[8], G9P[8], and G9P[6], have been reported in the USA[]. Similarly, G1P[8] has been reported to be the most frequent genotype in most European countries[]. Overall, G1P[8], G2P[4], […]

library_books

Phenotypic co receptor tropism and Maraviroc sensitivity in HIV 1 subtype C from East Africa

2018
Sci Rep
PMCID: 5799384
PMID: 29403064
DOI: 10.1038/s41598-018-20814-2

[…] , this algorithm has shown a limited sensitivity for the co-receptor tropism prediction in actual clinical samples (Reviewed in). Currently, the most widely used GTT tools are WebPSSM and Geno2Pheno (G2P), which assess the entire V3-loop sequence and assign the viral tropism by a more complex algorithm. However, all the machine-learning GTT tools have been developed primarily for HIV-1B and are no […]

library_books

Analysis of NSP4 Gene and Its Association with Genotyping of Rotavirus Group A in Stool Samples

2018
PMCID: 5712384
PMID: 28693095
DOI: 10.22034/ibj.22.1.42

[…] ctions in RV particles play an important role in the evolution of these viruses[]. There is a strong association between P and G typing with E typing in RV samples.Gene association G1, 9/P[8]/E1, and G2P[4]/E2 were detected, and no inter-genogroup reassorting containing VP7, VP4, and NSP4 occurred in these conventional strains.Based on previous epidemiological studies from Iran[-], there is a rare […]

library_books

Porcine rotavirus C in pigs with gastroenteritis on Thai swine farms, 2011–2016

2018
PeerJ
PMCID: 5947060
PMID: 29761045
DOI: 10.7717/peerj.4724

[…] ,000 pseudo-replicates implemented in MEGA6 software (). Bootstrap values >85% were considered significant for the VP7 gene and >80% for the VP4 gene. Prototypic RVC strain Cowden (G1P[1]), Shintoku (G2P[3]), HF (G3, undetermined P) and Bristol (G4P[2]) served as reference strains. […]

library_books

Prediction of HIV 1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time

2017
PLoS Comput Biol
PMCID: 5669501
PMID: 29065122
DOI: 10.1371/journal.pcbi.1005789

[…] ved from CATNAP [81]. For the trend analysis, we provide the accession numbers of each considered HIV-1 variant in the Los Alamos HIV sequence database [48] in S9 Table.At https://github.com/annahake/g2p-bnab, we additionally provide the computed kernels for the final models as well as the resampling instance for the 10 runs of stratified 5-fold cross-validation. As mentioned in the Conclusion, th […]


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G2P institution(s)
Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK; Departamento de Ingenieria de la Informacion y las Comunicaciones, Universidad de Murcia, Murcia, Spain; Department of Medical & Molecular Genetics, School of Medical Sciences, King's College London, Guy's Hospital, London, UK; Genomics England, Genomics England, Queen Mary University of London, London, UK; Department of Medical Biotechnology and Translational Medicine, Universita degli Studi, Milan, Italy; Department of Haematology, University of Cambridge, Cambridge, UK
G2P funding source(s)
Supported by the UK Medical Research Council (MRC) through the award of Tenure-track Clinician Scientist Fellowship to Mina Ryten (MR/N008324/1); by the Alzheimer’s Research UK through the award of a PhD Fellowship (ARUK-PhD2014-16), and by an award of a Leonard Wolfson Doctoral Training Fellowship in Neurodegeneration.

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