Scoring an alignment We have spent lots of time on amino acid similarity, and we have even used this knowledge in a rather sloppy manner to align some sequences. However, if we want to automate this we need to be a bit more formal. Well by now, you know that that depends on the structure, but we have no strucure, and we cannot really predict it either. So, determining which is the best of these two alignments must be done from sequence alignment alone. I suggest we split the group in a few teams thet try different strategies.
Lets discuss strategies in a round table discussion, and after that, simply work it out.
Click here to start the alignment program. 8.3 Examples that your alignment program should do correctly All five examples should be done corrrectly with the same scorings matrix.