Talk:Canavan Task 6 - Sequence-based mutation analysis

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Feedback:

Your entry is very well written and also good structured. I liked that you put the main aspect on the SNPs (instead of the methods, like we did in our wiki) so that you evaluated all methods on one SNP after another and then went on for the next SNP. This may be bad to see how good each of the method "performs" but your table in the conclusion shows this. Maybe you should have written a final conclusion sentence, e.g. which method you'd recommend to use.

"Though sometimes you are a bit repetitive (e.g. lowest scores/probabilities in the matrices). [Bernhoferm]"

I don't think this is a problem, I like this because I often forget these values and am reminded of this by the repetitive announcement. --Joerdensv 09:18, 19 June 2012 (UTC)


I've read your wiki up to and including R71K as you seem to be still working on the rest. So far I liked your wiki very much. You write the important details without too much "gibberish". The two tables in the beginning (mutations and phys.chem.properties) are also very clear. It's also a nice variety that you have a section for each mutation and not (like us^^) one for each analysis method. Though sometimes you are a bit repetitive (e.g. lowest scores/probabilities in the matrices). --Bernhoferm 16:57, 18 June 2012 (UTC)


One question:

I didn't make the Polyphen2 part in our task, so I don't know the exact output. Sometimes your write:

  • "This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)".

Wouldn't that mean that while all predictions are true positives (spec. 100%) you get no positives (sens. 0%)? Or is it a spelling error? --Bernhoferm 17:01, 18 June 2012 (UTC)


Corrections/Suggestions:

  • You have included PAM1, but are missing PAM250.
  • SNAP is missing, too.
  • You sometimes write blossum instead of blosum. I did the same sometimes at first^^
  • "Only looking at the location of the mutation almost at the C-terminus one would not expect structural or functional implications, since the mutant residue is far away from the known active site or the dimer interface." Something seems missing. Maybe a "being" between "mutation" and "almost"?
  • "Eventhough" (G123E, location) => "Even though"
  • "Furthermore, since Glycin is not involved in any interactions, there are thus no interactions that are be lost due to the mutaion." I would leave out the "thus".
  • "protperties", "smalles", "Blosum64", "glycin" (G123E)
  • "This goes along with the annotation for this mutation, that is not classifies as disease causing." (R71K)


Hello and thanks a lot! Yes, we're still at it.

  • Spelling mistakes already noticed before actually reading this ;-), and taken care of
  • PolyPhen scores corrected! Thanks a lot! Looked at the wrong option (HumDiv vs HumVar) - we're a mendelian disease.
  • SNAP (calculating) and PAM250 coming up.
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