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Polymorphism Phenotyping PolyPhen-2

Predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. For a mutation, PolyPhen calculates Naïve Bayes posterior probability that this mutation is damaging and reports estimates of false positive and true positive rates. Majority of these features involve comparison of a property of the wild-type allele and the corresponding property of the mutant allele, which together define an amino acid replacement.

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PolyPhen-2 classification

  • Animals
    • Homo sapiens

PolyPhen-2 specifications

Interface:
Web user interface
Input data:
A protein sequence
Computer skills:
Basic
Stability:
Stable
Maintained:
Yes
Restrictions to use:
Academic or non-commercial use
Input format:
FASTA
Version:
2.2.2
Source code URL:
http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-2.2.2r405c.tar.gz

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PolyPhen-2 classification

  • Animals
    • Homo sapiens

PolyPhen-2 specifications

Software type:
Package/Module
Restrictions to use:
Academic or non-commercial use
Input format:
FASTA
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Input data:
A protein sequence
Operating system:
Unix/Linux, Mac OS
Version:
2.2.2
Maintained:
Yes

PolyPhen-2 distribution

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PolyPhen-2 support

Documentation

Maintainer

  • Shamil R Sunyaev <>
  • Shamil R Sunyaev <>

Credits

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Publications

Institution(s)

Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA; Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany; Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Life Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA; European Molecular Biology Laboratory, Heidelberg, German

Funding source(s)

This work was supported by National Institutes of Health Grant R01 GM078598.

Link to literature

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