• Return midterm
  
  How to find pseudogenes?
  Discuss rooted and unrooted trees with four OTUs on whiteboard
  
  
• Discuss Friday's computer lab
  
  

Output from Glimmer

Output from ORF finder:

Note: Two ORFs that are not recognized by glimmer, and that have no recognizable homologs in the databank.
Note 2: Use alternative Initiation codons.

• Discuss failure of first principle approaches, example Exon finding:

In higher Eukaryotes the coding sequence is often interrupted by introns. Genes are transcribed into RNA. With the help of so-called spliceosomes introns are removed from the RNA and the exon portions are religated. In Arabidopsis the splice site consensus is as follows (from www.arabidopsis.org/info/splice_site.pdf):

(This table summarizes the sequences surrounding the intron splice sites in the plant Arabidopsis. E.g., in 52.9% of the intron exon boundaries (bottom part) the first base of the exon is a G, and in 40.5% the next nucleotide is a T.)

Given the many introns known in Arabidopsis, and the fact that all of the spliceosomal RNAs have been sequenced, one might expect that given the sequence of a primary transcript it would be possible to recognize with high reliability which parts of a sequence are coding.

• Discuss Hennig's approach towards a natural taxonomy:
  mono-, poly-, paraphyletic groups
  shared derived versus shared primitive characters
  Discuss examples from insects taxonomy, prokaryotes, protzoa
  
  
• Discuss slides (pdf version is here), including and especially the same/different tree link