PON-P2 – Predict Pathogenicity of Amino Acid Substitutions

PON-P2

:: DESCRIPTION

PON-P2 predicts the pathogenicity of amino acid substitutions. It is a machine learning-based approach and utilizes amino acid features, Gene Ontology (GO) annotations, evolutionary conservation, and if available, annotations of functional sites.

::DEVELOPER

Protein Structure and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

PLoS One. 2015 Feb 3;10(2):e0117380. doi: 10.1371/journal.pone.0117380. eCollection 2015.
PON-P2: Prediction Method for Fast and Reliable Identification of Harmful Variants.
Niroula A1, Urolagin S1, Vihinen M

WGPA – Web-based Gene Pathogenicity Analysis

WGPA

:: DESCRIPTION

WGPA is a web-based tool to analyse genes impacted by mutations and rank them through the integration of existing prioritisation tools, which assess different aspects of gene pathogenicity using population-level sequence data.

::DEVELOPER

WGPA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Web-based Gene Pathogenicity Analysis (WGPA): A web platform to interpret gene pathogenicity from personal genome data.
Diaz-Montana JJ, Rackham O, Diaz-Diaz N, Petretto E.
Bioinformatics. 2015 Oct 21. pii: btv598.

DANN – Annotating Pathogenicity of Genetic Variants

DANN

:: DESCRIPTION

DANN is a deep learning approach for annotating the pathogenicity of genetic variants.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/MacOsX
Python

:: DOWNLOAD

DANN

:: MORE INFORMATION

Citation

DANN: a deep learning approach for annotating the pathogenicity of genetic variants.
Quang D, Chen Y, Xie X.
Bioinformatics. 2015 Mar 1;31(5):761-3. doi: 10.1093/bioinformatics/btu703.

CADD 1.6 – Estimating the Relative Pathogenicity of human Genetic Variants

CADD 1.6

:: DESCRIPTION

CADD (Combined Annotation Dependent Depletion) is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.

::DEVELOPER

Shendure Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CADD

:: MORE INFORMATION

Citation

Nat Genet. 2014 Mar;46(3):310-5. doi: 10.1038/ng.2892. Epub 2014 Feb 2.
A general framework for estimating the relative pathogenicity of human genetic variants.
Kircher M1, Witten DM2, Jain P3, O’Roak BJ1, Cooper GM4, Shendure J5.