Which one of the following is true for PAM250 Scoring Matrix?
Which one of the following is true for PAM250 Scoring Matrix?
Select an option to attempt
Correct Answer: Option B
Explanation
PAM250 scoring matrix — evolutionary model for distant sequences:PAM (Point Accepted Mutation) matrices were developed by Margaret Dayhoff based on evolutionary models:• PAM1: model matrix for 1 accepted point mutation per 100 amino acids (very recent divergence).• PAM250: mathematical extrapolation of PAM1 raised to the 250th power → represents the expected amino acid substitution frequencies after 250 million years of evolution (distant relationships).Key properties:• Based on an EVOLUTIONARY MODEL: how amino acids change over LONG evolutionary time periods.• Appropriate for aligning DISTANTLY RELATED protein sequences.• For nucleotide sequences or synonymous/non-synonymous distinction: use different tools (e.g., dN/dS analysis, nucleotide substitution matrices).• Structural database searches: structure-based matrices (e.g., GONNET, BLOSUM) may be preferred.Contrast: BLOSUM62 is derived empirically from aligned conserved blocks; PAM250 is derived from evolutionary models. Both are used for protein alignment.Answer: PAM250 is based on evolutionary models predicting amino acid change frequencies over long evolutionary distances (250 accepted mutations per 100 aa).