What is a PolyPhen score?
The PolyPhen score represents the probability that a substitution is damaging, so values nearer one are more confidently predicted to be deleterious (note that this the opposite to SIFT). The qualitative prediction is based on the False Positive Rate of the classifier model used to make the predictions.
What is PolyPhen?
PolyPhen (=Polymorphism Phenotyping) 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 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.
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 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. This score represents the probability that a substitution is damaging.
What is a high CADD score?
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 a PolyPhen 2 score?
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 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 nsSNPs?
Non-synonymous single nucleotide polymorphisms (nsSNPs) are single base changes leading to a change to the amino acid sequence of the encoded protein.
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 become a CADD?
How can I obtain CADD scores? CADD scores are freely available for all non-commercial applications. If you are planning on using them in a commercial application, you can obtain a license through the UW CoMotion Express Licensing System.
Which is the correct score for PolyPhen-2?
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.
Which is the best PolyPhen-2 model to use?
The user can choose between HumDiv- and HumVar-trained PolyPhen-2 models. Diagnostics of Mendelian diseases requires distinguishing mutations with drastic effects from all the remaining human variation, including abundant mildly deleterious alleles. Thus, HumVar-trained model should be used for this task.
Which is more damaging PolyPhen-2 or sift?
0.15 to 1.0 — Variants with scores in this range are possibly damaging. 0.85 to 1.0 — Variants with scores in this range are more confidently predicted to be damaging. PolyPhen-2 and SIFT scores use the same range, 0.0 to 1.0, but with opposite meanings.
How is PolyPhen-2 used in protein prediction?
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.