There is great interest in characterizing the locations and functions of chemically modified bases in genomes. Bryan et al. report their Excision-seq method, in which DNA repair enzymes are used to cut genomic DNA at sites of the particular damaged bases they recognize, followed by high-throughput sequencing to characterize these cleavage sites. The researchers characterized the locations and sequence contexts of uracils (that is, demethylated thymines) in Escherichia coli and Saccharomyces cerevisiae genomes, and of ultraviolet-light-induced pyrimidine dimers in S. cerevisiae.