Practical Sections on Pairwise Alignments

Alignment Quiz

1. Complete the following dynamic programming matrix.
   (Assume PAM250 similarity values between residues: (H,K)=0, (K,K)=5, (K,R)=3, (H,R)=2 and as gapcost (-12))
   
   
   
   
   theory
   
   solution
   
   see also
   
   Alignment Applet
   
   

2. Wich kinds of gap penalties do you know?
   
   theory
   
   
3. Describe where to begin with backtracking, if gaps at the right end of an alignment aren't penalized.
   
   theory
   
   
4. Is the best Waterman-Eggert alignment a global or a local alignment?
   
   theory
   
   

5. Given the distance function d = u + 2g. Find out the similarity function s, so that the minimization in distance coincides with maximization in similarity.

   
   
   theory
   
   solution