Alignment statistics

Exercises

1. A score of 117 has a significance of 0.0001.
   What's the E-value, if this score is found in a database of 100,000 sequences?
   
   
   theory
   
2. sim.c finds the best non-intersecting alignments between two sequences
   or within one sequence.
   Download sim from the ftp-Server at EBI, where it is located
   in the directory /pub/software/unix/ and compile it.
   
   
3. Apply it to the yeast hexokinase A and the yeast hexokinase B protein
   (compare to exercise 2 at 'Pairwise sequence comparison' section)
   and calculate a value for the statistical significance of the local alignment.
   (note: how to run sim on protein sequences is explained in the code itsself)
   
   
   theory
   
4. The ToPLign-Server at GMD provides several alignment-tools.
   Use the ToPLign-Server to produce parametric alignments with the
   yeast hexokinase A and the yeast hexokinase B protein
   (i.e. choose the opening- and the extension-gap-penalty as parameters)
   
   
5. Obtain the alignments and the corresponding color-coded Path- and Confidence-Profiles.