PolyPhen specifications

Information


Unique identifier OMICS_00136
Name PolyPhen
Alternative name Polymorphism Phenotyping
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


  • Animals
    • Homo sapiens

Documentation


Maintainer


  • person_outline Shamil R Sunyaev <>

Information


Unique identifier OMICS_00136
Name PolyPhen
Alternative name Polymorphism Phenotyping
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


  • Animals
    • Homo sapiens

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Shamil R Sunyaev <>

PolyPhen articles

PolyPhen citations

 (10)
2017
PMCID: 5615344

[…] snvs were extracted based on the frequency of alleles in 1000 genome project [6] and exac database [11], and the deleteriousness was determined by three annotation tools: snpeff v4.11 [12], polyphen v2.2.2 [13], and cadd v1.3 [14]. coding cnvs were extracted by taking overlap between all the cnvs and exons on the human genome. segregation of substitution mutations and small deletions […]

2016
PMCID: 5014798

[…] mutation at position 1457 of the abcc8 protein is rare and causes a substitution of alanine with threonine (please see fig. s1 in the supplementary material). the online software polyphen-2 (polymorphism phenotyping v2, boston, harvard, ma, usa), applied for prediction of protein structure [12], showed high probability of an adverse effect of the ala1457thr mutation on the product […]

2016
PMCID: 4832069

[…] sanger's dna sequencing. conservation scores of novel variants were assigned a maximum score of 1 using phastcons29 to quantify conservation in reference to 33 mammalian taxa. mutation taster30 and polyphen-2 (ref. 31) softwares were used to predict the effect of protein-altering variants on protein structure and function. gene ontology and tissue expression for each variant was summarized […]

2015
PMCID: 4580363

[…] (consensus cds, refseq, ensembl and ucsc [38]). amino acid changes were determined based on the longest gene transcript. somatic nonsynonymous single-nucleotide mutations were analyzed using polyphen2 [39] in order to predict their impact on the protein function. to identify significantly mutated genes, the smg test in the genome music (mutational significance in cancer) suite was used […]

2015
PMCID: 4526773

[…] were as recommended by the manufacturers (pyromark q96 id, diatech pharmacogenetics, jesi, italy). a blast search on ncbi, cosmic and ucsc databases was performed for all identified variants. the polyphen-2 tool (genetics.bwh.harvard.edu) was consulted to define the putative effect of fa discovered variants, predicting the possible impact of the amino acid substitutions on the structure […]

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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