How does PolyPhen 2 work?
How does PolyPhen 2 work?
PolyPhen-2 identifies homologues of the input sequences via BLAST search in the UniRef100 database. The set of BLAST hits is filtered to retain hits that have: sequence identity to the input sequence in the range 30-94%, inclusively, and. alignment with the query sequence not smaller than 75 residues in length.
What is HumDiv and HumVar?
HumDiv: Mendelian disease variants vs. divergence from close mammalian homologs of human proteins (>=95% sequence identity). HumVar: all human variants associated with some disease (except cancer mutations) or loss of activity/function vs.
What is the meaning of polyphen2?
PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.
What is LRT score?
The likelihood ratio test (LRT) is a statistical test of the goodness-of-fit between two models. A relatively more complex model is compared to a simpler model to see if it fits a particular dataset significantly better. If so, the additional parameters of the more complex model are often used in subsequent analyses.
What does a high CADD score mean?
Like explained above, a scaled C-score of greater of equal 10 indicates that these are predicted to be the 10% most deleterious substitutions that you can do to the human genome, a score of greater or equal 20 indicates the 1% most deleterious and so on.
What is predict SNP?
PredictSNP: Predict SNP effect! Consensus classifiers for prediction of disease-related mutations. Consensus classifier for prediction of the effect of amino acid substitutions. Consensus classifier for prediction of the effect of nucleotide substitutions.
How do you cite PolyPhen?
If you publish research that uses polyphen you have to cite it as follows: Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. Nat Methods 7(4):248-249 (2010).
What is a significant CADD score?
What is a Grantham score?
The Grantham score attempts to predict the distance between two amino acids, in an evolutionary sense. A lower Grantham score reflects less evolutionary distance. A higher Grantham score reflects a greater evolutionary distance.
What is synonymous SNP?
A synonymous SNP is a coding SNP that does not change the protein sequence. A non-synonymous SNPT is one that changes the protein sequence.
What is a good PolyPhen-2 score?
PolyPhen-2 score The PolyPhen-2 score predicts the possible impact of an amino acid substitution on the structure and function of a human protein. The PolyPhen-2 score ranges from 0.0 (tolerated) to 1.0 (deleterious). PolyPhen-2 and SIFT scores use the same range, 0.0 to 1.0, but with opposite meanings.
What is the difference between SIFT and PolyPhen-2?
PolyPhen-2 and SIFT scores use the same range, 0.0 to 1.0, but with opposite meanings. A variant with a PolyPhen-2 score of 0.0 is predicted to be benign.
What is polypolyphen-2 and how does it work?
PolyPhen-2 is an automatic tool for prediction of possible impact of an amino acid substitution on the structure and function of a human protein. This prediction is based on a number of features comprising the sequence, phylogenetic and structural information characterizing the substitution.
What is polypolyphen-2 (poly morphism phenotype V 2)?
PolyPhen-2 ( Poly morphism Phen otyping v 2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. Please, use the form below to submit your query.
