Geno2pheno statistics

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Tool usage distribution map

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Associated diseases

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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 in publications

 (184)
PMCID: 5905485
DOI: 10.1093/ve/vey010.040

[…] pcr products were purified and subsequently sequenced with the 3130xl abi prism genetic analyzer. sequences were finally aligned and edited using chromaspro v1.7.6, and analyzed online with hcv.geno2pheno.org. ns5a rass were present in 28.4 per cent (23/81) of all gt1 infected patients, with gt1a showing the highest prevalence followed by gt1b (17 vs. 11 per cent, respectively). major ns5a […]

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 […]

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

[…] 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 […]

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

[…] 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., spss ver. 20 (ibm corporation, armonk, ny, usa) was used as tool for statistical analysis. categorical data were analyzed using the chi-square test or fisher’s exact test […]

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

[…] 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 […]


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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