Talk:Fabry:Sequence-based mutation analysis
From Bioinformatikpedia
Praise
- Nice tables
- Nice visualizations of the mutated residues. Is this pymol?
- Plenty of physicochemical properties.
Criticism
- Does the secondary structure prediction refer to the sequence before or after the mutation?
- What are your reasons for taking into account the substitution score of PAM1 and PAM250? Is the evolutionary distance not too short and too far, respectively?
- I think the substitution scores of the three matrices are not directly comparable. PAM1 should have lower scores than PAM250 relative to the maximum score.
- What do the entries in the PSSM table mean? It is obviously not the substitution score. In case of P40S: is P(P|40) = 0.81 or P(S|40) = 0.81?
- You classify the features either as disease causing or not disease causing. But what if a feature is in between?
- You are weighting each feature equally. For instance PAM1, PAM25, and BLOSUM62 are treated equally. The three secondary structure prediction are of course not independent.
