PolyPhen protocols

PolyPhen specifications

Information


Unique identifier OMICS_00136
Name PolyPhen
Alternative names Polymorphism Phenotyping, PolyPhen-2
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A protein sequence
Input format FASTA
Output data A prediction of probably damaging, possibly damaging, or benign, along with a numerical score ranging from 0.0 (benign) to 1.0 (damaging).
Computer skills Basic
Version 2.2.2
Stability Stable
Source code URL http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-2.2.2r405c.tar.gz
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainer


  • person_outline Shamil R Sunyaev <>

Information


Unique identifier OMICS_00136
Name PolyPhen
Alternative names Polymorphism Phenotyping, PolyPhen-2
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A protein sequence
Input format FASTA
Output data A prediction of probably damaging, possibly damaging, or benign, along with a numerical score ranging from 0.0 (benign) to 1.0 (damaging).
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 2.2.2
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Shamil R Sunyaev <>

Publications for Polymorphism Phenotyping

PolyPhen IN pipelines

 (17)
2018
PMCID: 5813894
PMID: 29447163
DOI: 10.1371/journal.pgen.1007194

[…] cbioportal’s normalized rnaseq z-scores., we examined snp-based linkage via ldlink, ldproxy [47] using the ceu population for reference. the functional predictions for missense snps were scored by polyphen [22] and the regulation was scored by haploreg (v4) [48] using the eur reference and its default position weight-matrix scoring algorithms [49]., expected frequencies under the autosomal […]

2018
PMCID: 5858179
PMID: 29556353
DOI: 10.7150/thno.22010

[…] other confounding covariates taken into account. mutsigcl and mutsigfn measure the significance of hotspot mutations and functional impacts of mutations, respectively. in mutsigfn analysis, cadd and polyphen2 scores available from dbnsfp database were separately used 37. for efficient computation, a two-step permutation was carried out, in which 999 times were performed in the first step […]

2017
PMCID: 5259721
PMID: 28117402
DOI: 10.1038/srep41188

[…] 10,252 genes. of 94,369 snvs, 21,235 were non-synonymous (ns) affecting 9444 protein coding genes, including 313 that caused the gain or loss of a stop codon and 6,541 that were considered by polyphen-26 as being damaging (supplementary fig. 1)., fisher’s exact test and logistic regression using between 1 and 10 covariates were performed using plink7 […]

2017
PMCID: 5286855
PMID: 28180184
DOI: 10.1212/NXG.0000000000000129

[…] database and the genome aggregation database (gnomad). variants predicted to be damaging by the combined annotation dependent depletion (cadd) tool or to disrupt protein structure or function by polymorphism phenotyping v2 (polyphen2) algorithms were considered as candidate genes responsible for the child's phenotype., rat gluk2a(a657t) and neto2 complementary dnas (cdnas) were provided […]

2017
PMCID: 5286855
PMID: 28180184
DOI: 10.1212/NXG.0000000000000129

[…] database (gnomad). variants predicted to be damaging by the combined annotation dependent depletion (cadd) tool or to disrupt protein structure or function by polymorphism phenotyping v2 (polyphen2) algorithms were considered as candidate genes responsible for the child's phenotype., rat gluk2a(a657t) and neto2 complementary dnas (cdnas) were provided by michisuke yuzaki (keio […]

PolyPhen institution(s)
Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA; Program in Biophysics, Harvard University, Cambridge, MA, USA

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