Table 2 Bioinformatics tools used for the prediction of potential pathogenic effects of protein-coding variants
From: Analysis of genomic ancestry and characterization of a new variant in MPS type VII
Name | Main algorithm | Input data |
|---|---|---|
PolyPhen | Provides information on the substitution site, phylogenetic and structural effects of the nsSNP | FASTA protein sequence, mutation |
SIFT | Selects relevant proteins and align to determine the conservation level | FASTA protein sequence, mutation |
PROVEAN | Measures the difference in sequence similarity before and after a mutation, based on alignment | UniProt ID, mutation |
Mutation Taster | Evaluates variant pathogenicity using multiple databases, disease associations, homology modelling, and protein features | Gene identification, Ensembl transcript id, nucleotides around the mutation |
HOPE | Analyses point mutations using BLAST, 3D structure calculations, UniProt annotation, and homology modelling | FASTA protein sequence, mutation |