Tag: Amino Acid Substitution

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

  NO

:: 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

ASaturA – Discriminate Amino Acid Substitutions

ASaturA

:: DESCRIPTION

ASaturA discriminates amino acid substitutions with high and low probabilities of occurrence.ASaturA sorts all substitutions according to these probabilities and a probability ‘cut-off’ value can be chosen that differentiates between frequent and rare substitutions. For each sequence pair, the program plots the number of observed frequent and rare aa replacements against their evolutionary distance. By modifying the substitution probability ‘cut-off’ value, the number of aa substitutions classified as frequent or rare can be changed. Ideally, careful selection of the ‘cut-off’ value splits the original data set into a saturated and an unsaturated one. Besides the most widely used substitution probability matrices, such as PAM, BLOSUM, mtREV24 and JTT, user-defined matrices can be used also.

::DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 ASaturA

:: MORE INFORMATION

Citation:

Van de Peer, Y., Frickey, T., Taylor, J.S., Meyer, A. (2002)
Dealing with saturation at the amino acid level: A case study involving anciently duplicated zebrafish genes.
Gene 295, 205-11.

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