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Online Lectures on Bioinformatics

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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))



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    solution

    see also
    Alignment Applet
    Alignment Applet


  2. Wich kinds of gap penalties do you know?

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  3. Describe where to begin with backtracking, if gaps at the right end of an alignment aren't penalized.

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  4. Is the best Waterman-Eggert alignment a global or a local alignment?

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  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.


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    solution

Comments are very welcome.
luz@molgen.mpg.de