Figure 1: A schematic representation of the computational method.
From: Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution
The drawing shows a hypothetical alignment between two retrotransposons that has several mismatches, most of which are G-to-A. To detect editing, we scan the alignments for long clusters of G-to-A mismatches not separated by any other mismatch. We then calculate the probability that such a cluster (having k G-to-A mismatches over a subsequence of length n) occurred by chance, based on the probabilities of C-to-T and T-to-C transitions (Methods).
