I’m working on a project to estimate evolutionary parameters using an EM algorithm that sums over all possible alignments. I’m working on revising a separate paper and have decided to make a quick estimation of some parameters and use them in some simulations. This is what I got today:
Expected number of substitutions between humans and mice:
0.478222 sub/nuc
Rate of gap formation:
0.213542 gap/sub
Slope parameter for power-law distribution of gap sizes:
1.80675
These parameters were estimated by comparing the sequences of Intron 7 of Mouse ADH1 gene and Intron 7 of Human ADH1c gene. They give us a clue into the underlying mutational process that has affected the genomes since the species diverged.
