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so we were talking about how you score alignments and you score sequences right and we had an example of a sequence alignment that looked like this and when we added up the scores for each amino acid pair based off of blosum62 and when we accounted for the gap that we have to insert in the alignment to make the alignment correct we had a score of I believe 44 so so thatamp;#39;s our raw score which is just a number that kind of doesnamp;#39;t really relate to anything right we call that the score and we can convert from the score we can convert to a bit score and the bit score normalizes to a couple of different factors so the bit score s sorry s prime is lambda times the raw score minus the natural log of K divided by the natural log - so this is a whatamp;#39;s called our bit score and weamp;#39;re normalizing it and so here weamp;#39;ve got two constants lambda and K and theyamp;#39;re both dependent the both dependent on the scoring matrix that we use and theyamp;#39;re depe
