Pam and blosum matrices pdf

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It only takes a minute to sign up. Connect and share knowledge within a single location that is structured and easy to search. By using the scoring matrix substitution matrix to score the comparison of each residue pair, there are 20 3 possible match scores for a 3-letter word.

I do not understand how they got a score of 15 for PQG v. What is a scoring matrix, how is it computed, and how is it used? Each of them has a score for every possible alignment combination between the 20 standard amino acids 1. They both do more or less the same job but have been derived using different approaches. The score for a given pair of amino acids aligning with each other is the log-odds score measuring how often this particular alignment is found and how often it would be expected to be found by chance:.

In simple words, the BLOSUM matrices give you a score based on how often the alignment you observe in your sequences is found in alignments of similar sequences. This is a nice middle ground and will do for most cases.

The PAM matrices are built using a different approach. Next, a score for the alignment of all possible pairs of amino acids is calculated based on its observed frequency in the aligned proteins. Then, the scores are extrapolated to alignments of different sequence similarity using mathematical tools.

The PAM matrices assume a model of protein evolution and score the alignments based on that model. The PAM-I matrix is the only one that was actually built from real alignments. With all that in mind, the scoring matrices are used by BLAST to calculate the score of the alignment. You can think of this score as the sum of the scores of each individual pair of aligned amino acids in your BLAST result.