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Table 1 Bioinformatics tools for in silico analysis

From: In silico analysis of missense mutations in exons 1–5 of the F9 gene that cause hemophilia B

Program Based on Prediction Score Functional impact (reference) Available at
Poly Phen 2* Sequence- and structure-based approach Benign < 0.5 On the structure and function of a human protein [19] http://genetics.Bwh.harvard.edu/pph2/index.shtml
Possibly damaging ≥0.5
Probably damaging
SIFT Sequence-based approach Tolerated ≥0.05 On protein function and the physiochemical properties of AA [20]. http://sift.jcvi.org/
Damaging < 0.05
PANTHER Sequence-based approach Probably benign 0 to −3 Estimates the likelihood of a particular nonsynonymous coding SNP causing a functional impact on the protein [21]. http://www.pantherdb.org/tools/csnpScoreForm.jsp
Possibly damaging <−3
Probably damaging
MutationAssessor Sequence-based approach neutral ≤0.8 On the substitution of AA in the protein by assessing evolutionary conservation [22]. http://mutationassessor.org
low impact 0.8 to < 1.9
medium impact 1.9 to ≤3.5
high impact > 3.5
PROVEAN Sequence-based approach Neutral > − 2.5 On the biological function of a protein [23]. http://provean.jcvi.org/index.php
Deleterious <−2.5
SNAP2 Sequence- and structure-based approach Neutral 100 On the secondary structure and compares the solvent accessibility of the wild and mutated protein [24]. https://rostlab.org/services/snap2web
Effect − 100
  1. *, “HumDiv” is the default Classifier model used by probabilistic predictor; it is preferred for evaluating rare alleles, dense mapping of regions identified by genome-wide association studies, and analysis of natural selection. “HumVar” is better suited for diagnostics of Mendelian diseases, which requires distinguishing mutations with drastic effects from all the remaining human variation, including abundant mildly deleterious alleles
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