Group meeting feedback

• Taylor
  • we might want to be more careful about terminology clashes
    • we use piLoci and miLoci to refer to protein-coding iLoci and merged iLoci, respectively
    • in molecular genetics the pi- and mi- prefixes are often associated with piwi and microRNAs, respectively
    • it may not be a big deal, but it's something to consider
  • yeast is arguably the best annotated eukaryotic genome, should really investigate its organization
  • effect of TEs?
  • annotated UTR length and delta parameter
    • different deltas for upstream and downstream could be useful in some contexts
    • might think about how/whether UTR length could influence delta gene-by-gene
• Volker
  • did a project a few years ago
    • found pairs of genes with opposite orientation (i.e. <-- -->)
    • looked for palidromic motifs in the intergenic space
    • could be potentially interesting to investigate
  • read up on r-scans (maybe this is a good starting point)
  • likes the idea of simulation
    • keep genome content constant, but modulate organization
    • randomly place giLoci in genomic sequence (don't allow overlaps)
    • compare miLocus/iiLocus summary stats
      • length distributions
      • miLocus gene counts
      • r-scans

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