Talk:Fabry:Sequence-based mutation analysis

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Revision as of 21:01, 18 June 2012 by Staniewski (talk | contribs) (Praise)

Praise

  • Nice tables
  • Nice visualizations of the mutated residues. Is this pymol?
I don't think so. They were generated by HOPE.
  • Plenty of physicochemical properties.

Criticism

  • Does the secondary structure prediction refer to the sequence before or after the mutation?

--> Since we used the files from Task 3 (see Journal), it is from the native structure

  • 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?

--> We were said to do that

  • 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.

--> We díd compare them relatively not the absolute values

  • 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?

--> There are more severe forms of the disease and less severe forms, but either you are ill or not... What else is there 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.

--> but sometimes different. A weighting function would have actually been a good idea, but since we are not done yet, it would have made no sense to develop one.