Table 5.
Comparison of sequence mutation analysis tools based on types of datasets used for homology searches, and approaches they use for conservation analysis. List of structural features contributing to calculated conservation scores.
| METHOD | DATASETS FOR HOMOLOGY SEARCHES | PROTEIN STRUCTURES | CONSERVATION ANALYSIS | ||
|---|---|---|---|---|---|
| GENOMIC SEQUENCES | PROTEIN SEQUENCES | SEQUENCE ALIGNMENT | STRUCTURAL FEATURES | ||
| SIFT | – | Yes | – | PsiBlast | – |
| PROVEAN | – | Yes | – | Blastp | – |
| PolyPhen-2 | – | Yes | Yes | Blast MAFFT |
Yes*b,c |
| GeneSV | Yes | Yes | Yes | PsiBlast Smith-Waterman |
Yesa,b,c,d,e |
Notes:
a
accuracy of constructed structural models.
b
surface exposure (location of the mutation position: buried, exposed).
c
structural element (coil, helix, strand).
d
antigenic site (position within the epitope: yes, not).
e
structural conservation.
(*) – structure-based features are estimated from the analysis of closest homologs with known 3D structure (no structural models are constructed).