Difference between revisions of "Talk:Sequence Alignments Gaucher Disease"
From Bioinformatikpedia
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* I'm not sure about your evalutation of the hit list in pdb: You only report the overlap but don't use them as test set? |
* I'm not sure about your evalutation of the hit list in pdb: You only report the overlap but don't use them as test set? |
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** To which extend should we use the PDB hits as test set? Do you mean that we should have done a ROC analysis? As I wrote in the wiki, we would have needed a uniform test set for HHblits and blastpgp for being able to compare the different methods thoroughly. Another point is, that I do not really known how to classify the PDB hits as true positives and false positives. Did you find a good solution for that? |
** To which extend should we use the PDB hits as test set? Do you mean that we should have done a ROC analysis? As I wrote in the wiki, we would have needed a uniform test set for HHblits and blastpgp for being able to compare the different methods thoroughly. Another point is, that I do not really known how to classify the PDB hits as true positives and false positives. Did you find a good solution for that? |
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| + | *** Not really, it just sounded like you had one for PDB but didn't tell us. :) |
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* If I get the task description right, we are supposed to create 5 datasets for the alignments, as you have done. Only if this is not possible, 3 less strictly defined datasets can be used. |
* If I get the task description right, we are supposed to create 5 datasets for the alignments, as you have done. Only if this is not possible, 3 less strictly defined datasets can be used. |
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--[[User:Boidolj|Boidolj]] 18:38, 7 May 2012 (UTC) |
--[[User:Boidolj|Boidolj]] 18:38, 7 May 2012 (UTC) |
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Revision as of 20:29, 7 May 2012
Just out of interest (I'm not reviewing your page this week): How did you generate your Venn diagrams? I really like the way they look.
- We made use of this online tool.
I see, you're not finished with the alignment part yet, but a few comments:
- I'm not sure about your evalutation of the hit list in pdb: You only report the overlap but don't use them as test set?
- To which extend should we use the PDB hits as test set? Do you mean that we should have done a ROC analysis? As I wrote in the wiki, we would have needed a uniform test set for HHblits and blastpgp for being able to compare the different methods thoroughly. Another point is, that I do not really known how to classify the PDB hits as true positives and false positives. Did you find a good solution for that?
- Not really, it just sounded like you had one for PDB but didn't tell us. :)
- To which extend should we use the PDB hits as test set? Do you mean that we should have done a ROC analysis? As I wrote in the wiki, we would have needed a uniform test set for HHblits and blastpgp for being able to compare the different methods thoroughly. Another point is, that I do not really known how to classify the PDB hits as true positives and false positives. Did you find a good solution for that?
- If I get the task description right, we are supposed to create 5 datasets for the alignments, as you have done. Only if this is not possible, 3 less strictly defined datasets can be used.
--Boidolj 18:38, 7 May 2012 (UTC)
