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Biology
Posted 5 months ago
What are PAM and BLOSUM matrices used for and what is their difference?
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Answer from Sia
Posted 5 months ago
Solution
a
PAM matrices: PAM (Point Accepted Mutation) matrices are used to measure evolutionary distances between sequences. They are based on the probability of amino acid substitutions over a certain evolutionary time period
b
BLOSUM matrices: BLOSUM (BLOcks SUbstitution Matrix) matrices are used to score alignments between protein sequences. They are based on observed substitutions in blocks of local alignments of protein sequences
c
Difference: The main difference between PAM and BLOSUM matrices is that PAM matrices are based on evolutionary models and are extrapolated from closely related sequences, while BLOSUM matrices are derived from empirical data and are based on observed substitutions in more distantly related sequences
Answer
PAM and BLOSUM matrices are used for scoring alignments between protein sequences, with PAM focusing on evolutionary distances and BLOSUM on observed substitutions.
Key Concept
PAM and BLOSUM matrices are tools for sequence alignment in bioinformatics.
Explanation
PAM matrices are based on evolutionary models and measure evolutionary distances, while BLOSUM matrices are derived from empirical data and focus on observed substitutions.
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