for two related proteins, taken from organisms living today, is sought. The two proteins have both been accumulating accepted mutations since the date of divergence, and so the total number of mutations per amino acid separating them is approximately twice that which separates them from their common ancestor. If a range of PAM matrices are used to align two proteins that are known to be related, then the value of in the PAMn matrix which results in the best score is most likely to correspond to the mutations per amino acid separating the two proteins. Halving this value and dividing by the rate at which accepted mutations accumulate in the protein family provides an estimate of the time of divergence of these two proteins from their common ancestor. That is, the time of divergence in myr is Where is the number of mutations per amino acid, and is the rate of accepted mutation accumulation in mutations per amino acid site per million years. Use in BLAST PAM matrices are also used as a scoring matrix when comparing DNA sequences or protein sequences to judge the quality of the alignment. This form of scoring system is utilized by a wide range of alignment software including BLAST. Comparing PAM and BLOSUM Although the PAM log-odds matrices were the first scoring matrices used with BLAST, the PAM matrices have largely been replaced by the BLOSUM matrices. Although both matrices produce similar scoring outcomes they were generated using differing methodologies. The BLOSUM matrices were generated directly from the amino acid differences in aligned blocks that have diverged to varying degrees the PAM matrices reflect the extrapolation of evolutionary information based on closely related sequences to longer timescales. Since scoring information for the PAM and BLOSUM matrices were generated in very different ways the numbers associated with the matrices have fundamentally different meanings; the numbers for PAM matrices increase for comparisons among more divergent proteins whereas the numbers for the BLOSUM matrices decrease. However, all amino acid substitution matrices can be compared in an information theoretic framework using their relative entropy. See also Point mutation Sequence alignment Margaret Dayhoff Molecular clock BLOSUM BLAST References External links http://www.inf.ethz.ch/personal/gonnet/DarwinManual/node148.html http://www.bioinformatics.nl/tools/pam.html For quickly calculating a PAM matrix. http://web.expasy.org/docs/relnotes/relstat.html The most recent statistics from the Swiss-Prot protein knowledgebase. Section 6.1 contains the most up-to-date amino acid frequencies Mutation Bioinformatics