Geno2pheno statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Geno2pheno
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Tool usage distribution map

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Protocols

Geno2pheno specifications

Information


Unique identifier OMICS_12141
Name Geno2pheno
Interface Web user interface
Restrictions to use None
Input data Sequences
Input format FASTA
Computer skills Basic
Version 2.5
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Viruses
    • Human immunodeficiency virus 1
    • Human immunodeficiency virus 2

Maintainer


  • person_outline Nico Pfeifer

Publications for Geno2pheno

Geno2pheno citations

 (190)
library_books

Next generation sequencing provides an added value in determining drug resistance and viral tropism in Cameroonian HIV 1 vertically infected children

2018
PMCID: 5895385
PMID: 29595649
DOI: 10.1097/MD.0000000000010176

[…] PR/RT DRMs and HIV-1 co-receptor usage were interpreted using Stanford HIVdb list (updated March 9, 2015, available at http://hivdb.stanford.edu/pages/download/resistanceMutations_handout.pdf) and geno2pheno.v2.5 (http://coreceptor.geno2pheno.org/), respectively. Using a quantitative interpretation, viruses were considered CXCR4-tropic (X4-variants) by UDPS when ≥2% viral species had a false-po […]

library_books

Evaluation of the cobas® GT hepatitis C virus genotyping assay in G1 6 viruses including low viral loads and LiPA failures

2018
PLoS One
PMCID: 5864039
PMID: 29566005
DOI: 10.1371/journal.pone.0194396

[…] lary electrophoresis in a Beckman Coulter capillary electrophoresis CEQ 8000 system.Newly obtained sequences were first blasted against the whole nucleotide NCBI database []. The Max Planck Institute Geno2Pheno [HCV] tool was then used to confirm the genotype []. A final step of phylogenetic analysis was performed using the MAFFT alignment tool [] from the Japanese Computational Biology Research C […]

library_books

Genotyping and sero virological characterization of hepatitis B virus (HBV) in blood donors, Southern Ethiopia

2018
PLoS One
PMCID: 5819820
PMID: 29462187
DOI: 10.1371/journal.pone.0193177

[…] GenBank, to analyze presence of mutation within and outside the MHR. The mutation pattern was assessed based on published reports [, ]using BioEdit ver.7.2.5; for further confirmation, an online tool Geno2Pheno was also used. […]

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

[…] oop. However, 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-1 […]

library_books

Benzyl 2 Acetamido 2 Deoxy α d Galactopyranoside Increases Human Immunodeficiency Virus Replication and Viral Outgrowth Efficacy In Vitro

2018
Front Immunol
PMCID: 5810283
PMID: 29472913
DOI: 10.3389/fimmu.2017.02010

[…] e for each of the subject samples, using a neighbor-joining (NJ) approach and bootstrapping (n = 100) to obtain support information. Finally, all env sequences evaluated for co-receptor tropism using geno2pheno web service, using a FPR threshold of 10% (). […]

library_books

HIV 1 co receptor tropism and liver fibrosis in HIV infected patients

2018
PLoS One
PMCID: 5764264
PMID: 29324755
DOI: 10.1371/journal.pone.0190302

[…] r results did not change when adjusted for the method used to assess HIV tropism. In the majority (74%) of our patients, CRT was assessed by a genotypic method. Based on the HIV-1 gp120 sequence, the geno2pheno interpretation furnishes a FPR (false positive rate) which is a percentage score indicating the likelihood that a V3 sequence is falsely predicted as CXCR4-using patients. Therefore, patien […]


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Geno2pheno institution(s)
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
Geno2pheno funding source(s)
This work was supported in part by the Intramural Research Program of the NIAID, NIH, Bethesda, MD, USA.

Geno2pheno review

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matdoering

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Web
In contrast to the provided information, geno2pheno is still being actively maintained and is still available via geno2pheno.org