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  1. The amino acid substitution matrices in decreasing order of stringency for comparing protein sequences are
    1. PAM250, PAM120, PAM100
    2. PAM100, PAM120, PAM250
    3. PAM250, PAM100, PAM120
    4. PAM120, PAM250, PAM100
Correct Option: B

Substitution matrices like PAM100, PAM120 and PAM250 are constructed by observing the frequencies of amino acid replacements in large samples of protein sequences. For a given replacement, the PAM value is proportional to the natural log of the frequency with which that replacement was observed to occur. One PAM unit is defined as the
amount of sequence divergence corresponding to a 1% amino acid replacement rate. For closely-related sequences, it is appropriate to use a PAM100 matrix, in which PAM units have been extrapolated to 100% replacement. In other words, 100% of the positions show at least one replacement.  For most database searches, a PAM250 matrix is preferred, since larger databases will tend to have sets of more distantly-related sequences. So, decreasing order of stringency of point accepted mutation matrices would be: PAM100 > PAM120 > PAM250.



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