Difference between revisions of "Talk:Fabry:Sequence-based mutation analysis"
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(Created page with "== Praise == * Nice tables * Nice visualizations of the mutated residues. Is this pymol? * Plenty of physicochemical properties. == Criticism == * Does the secondary structure…") |
Rackersederj (talk | contribs) |
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== Criticism == |
== Criticism == |
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* Does the secondary structure prediction refer to the sequence before or after the mutation? |
* Does the secondary structure prediction refer to the sequence before or after the mutation? |
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| + | --> 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 |
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* 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 |
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* 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? |
* 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? |
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* You classify the features either as disease causing or not disease causing. But what if a feature is in between? |
* You classify the features either as disease causing or not disease causing. But what if a feature is in between? |
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| + | --> 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? |
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* 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. |
* 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. |
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| + | --> 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. |
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Revision as of 20:59, 18 June 2012
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?
--> 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.
