Talk:Canavan Task 2 - Sequence alignments

From Bioinformatikpedia
  • Your PSI-Blast search seems to have hit the reporting limits. Please increase the cutoffs, so you can really compare the results. andrea 10:32, 3 May 2012 (UTC)


  • Some figures are not referenced properly in the text, tables are not referenced or mentioned at all
  • Your cutoff for the blast searches seems very low, and I think you didn't increase the number of results like andrea wrote. My guess is that you consequently can not really compare the number of hits.
    • Agreed, this might also solve you problem of no pdb structures -jonas
  • You could have tried to use the whole big database for PSI-Blast and PDB for HHBlits to make the results more comparable.
  • You could elaborate a little bit more, e.g. on the MSA's.
  • I like your figures, very nice, just get rid of the ??.
  • Making the link to 3D structure is very interesting but I would have enjoyed reading more about it :)

I did not have the time to really rethink your approach in detail, but you worked nicely and especially very efficiently. Best, Alice

A few things in addition to what alice said

  • The red markings in the sequence at the beginning are explained only towards the very end
  • What does this figure signify?
  • I do not agree with your reasoning that it is unlikely to find another structure for a class of proteins, once one structure has been solved for them. In fact the knowledge of how to solve the structure gained from the first experiment might lead to a higher probability, that more structures e.g. of homologs in another species or mutants, will be solved


Thank you all for the detailled reviews! We'll have to admit that we started a bit late on this task, and therefore couldn't work out some things as we would have liked to.

We'll catch up with what you wrote here, and subsequently be hopefully to erase most or all of these comments :).

Regards, SuF