Difference between revisions of "Talk:Fabry:Sequence-based mutation analysis"
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Staniewski (talk | contribs) (→Criticism) |
Rackersederj (talk | contribs) (→Criticism) |
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--> Since we used the files from Task 3 (see Journal), it is from the native structure |
--> Since we used the files from Task 3 (see Journal), it is from the native structure |
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* 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? |
* 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? |
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− | --> We were said to do that |
+ | --> We were said to do that. At least that's how I understood it |
* 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. |
* 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. |
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--> We díd compare them relatively not the absolute values |
--> We díd compare them relatively not the absolute values |
Latest revision as of 21:23, 18 June 2012
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. At least that's how I understood it
- 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?
- It's the "weighted observed percentages rounded down" value as shown here. As I understood, it means that, e.g. for P40S, in 81% of the sequences, the wild type is conserved whereas in 2% of the sequences, the mutation (P → S) is observed.
- 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.