Assignment #6:
  1. Web Exploration Questions page 211 question 1.
  2. Web Exploration Questions page 211 question 2.
  3. Web Exploration Questions page 214 question 4.
  4. Web Exploration Questions page 214 question 5.
  5. Web Exploration Questions page 214 question 6.
  6. Web Exploration Questions page 214 question 7.
  7. use the ch7ex1.pl script found in ~clement/cs418/ch7 to predict alpha-helix structures in the sample amino acid sequence ch7ex1in.txt. Now find the amino acid sequence for an entry in PDB (try looking up 3E4B if you lack imagination). You can find the entry's amino acid sequence using the sequence tab at the top of the page. How well does the Chou-Fasman algorithm do at predicting alpha helices.
  8. The CATH database contains classifications of protiens according to their structure. Blast the 1oaiA00 domain against the CATH database to find other structures with similar sequences. How similar are the structures found with this blast to the original 1oaiA00 domain?
  9. Look up the p53 DNA-binding domain entry in PFAM. Click on the "288 sequences" glyph at the top of the page. Use Jalview to view the alignment of the seed members of the family. How similar are the sequences in this family? What percentage of the columns have identical amino acids for all 7 species in the seed?