Talk:Sequence-based predictions (PKU)

This is just a place to add criticism and or positive feedback so we Jonathan and Sebastian have a possibility to improve. Please note, that we wont be able to adress all matters immediately but we will address them eventually!

source: [1]

We also want to mention our slogan for this current teamwork

criticism

• There are several typos and some spelling mistakes still in the text, e.g. reagions, ver (instead of very), cant, ties, tree (instead of three) ... and so on. I found myself almost correcting some of those ;)

• The visual outputs of PsiPred are not discussed so might as well be left out

GOpet section

• The link within the table does not work, and the link in the text above is labelled gene-ontology.com although it is really AmiGO http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=UniProtKB:P00439
• You state that 7 of the predicted annotations are found within the 10 from AmiGO .... but I can not reproduce this (e.g. 0003824 is not in there). The AmiGO GO terms should not be viewed as a gold standard anyway but you explained the go terms assignment very well in the text.

positive feedback

• The calculated scores e.g. for the secondary structure prediction are very helpful to asses the performance of the methods. The scores are additionally well displayed.

• Altogether the wiki entry is very interesting and nice to read.

• nice that you gave an introduction to the task, (however you pretty much did it two times?)
• interesting idea to compare iupred short and long mode, thanks

suggestions

• You could consider removing either the first paragraph (In this task we will find out, how much information ...) or the task description and merging the contents as these two sections are a bit redundant.

• Some sentences seem a bit bewildering e.g. "Overall the results one can derive from several methods really are the same but one also can see the difference in the methods", but this may be just my perception.

• The source of the Uniprot structure is DSSP, this should actually be very easy to find: http://www.uniprot.org/manual/helix
• I understand your way of organising the scripts makes this a bit hard, but I strongly suggest a better seperation between protocol and evaluation
• try to adhere to a more scientific writing style, i.e. no 't tells you a lot and nothing' and so on