Online Lectures on Bioinformatics
Practical Sections on Pairwise Alignments
- 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))
- Wich kinds of gap penalties do you know?
- Describe where to begin with backtracking, if gaps at the right end of an alignment aren't penalized.
- Is the best Waterman-Eggert alignment a global or a local alignment?
Given the distance function
d = u + 2g. Find out the similarity
function s, so that the minimization in distance coincides
with maximization in similarity.
Comments are very welcome.