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Comments to the proposal talk on April 21

Here are some additional comments that haven't been made in the lecture:

David:
  • Slide 3: "The difference lies in the genome!"
    • Maybe rephrase to "is due to", maybe consult a dictionary? -- ManuelHoltgrewe - 22 Apr 2010
    • What about epigenetics, methylation, histone modifications?
  • Slide 4: "The big picture"
    • Please use a font at least as big as normal text.
    • Better use a hierarchy and stay in one domain.
    • Black on brown is hard to read. Use brighter text or fill colors.
  • Slide 6-8: The pictures (minor comments)
    • The reversal could simply be depicted with 2 arrows in opposing directions representing the same fragment.
    • The copied fragments could be highlighted by using the same color for original and copy fragments
  • Slide 10: "Orthologous and Paralogous"
    • The difference didn't become clear from the figure. An (additional) textual definition would be nice.
  • Slide 19: "Chaining"
    • If you explain how the chaining works, you should mention what the seeds are and where they come from.
  • Slides 21-24: "Genome Annotation"
    • The whole annotation talk needs more structure.
    • How to infer annotations?
    • What are the obstacles and what algorithms exist?

Manuel:
  • Evolution
    • In the alignment literature, the term "point mutation" is often used in the context of "Point Accepted Mutation" matrices which only account for substitution. Could you give some literature references for your usage? What is the source of your definition? What about splitting this out into "point mutation" and "indel"?
    • What about captions for the larger scale rearrangement slides and the images on the slides?
  • Homologous Orthologous and Paralogous
    • What about splitting this out into two pictures? I think this one is confusing.
  • Types Of Alignments:
    • The presentation should make clear that these are multiple sequence alignments, maybe draw one horizontal line for each sequence.
    • The point about glocal alignments is that they allow for non-collinear alignments. Is it useful to show only collinear alignments?
  • Algorithmic Approaches SuperMap:
    • Progressive Alignment and Chaning are very useful and popular concepts outside the context of SuperMap. Maybe your presentation should show this?

Comments to the slides in subversion

DavidWeese - 06 May 2010:
  • S20: "Suffixarrrays"
  • S20: Actually suffix array can only be used to find exact segments
  • S23: "with a edge"
FELIX: thanks, I corrected these

Comments

 
Topic revision: r5 - 07 May 2010, FelixHeeger
 
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