Distribution of Unique Sequences in the Human Genome

Programmable sequence-specific endonucleases are powerful tools for genome alteration with high precision. For example, the CRISPR system is an efficient tool for genome engineering in eukaryotic cells by simply specifying a 20-bp targeting sequence within its guide RNA. When studying large genomes, however, the design of target sequences is complicated by the redundancy of sequences. The distribution of unique sequences in the genome is of interest. In this paper, I describe the development of a novel method, UF, for detecting unique 20-bp sequences in entire genomes. UF stands for "Unique Finder". By using UF, the distribution of unique sequences in the human genome was investigated. It was found that 60% of the human genome is unique on average. However, non-unique regions of human genome are concentrated on centromeres and terminal regions of the chromosomes. The proportions of unique sequences are about 80% in the rest part of the genome. The program for obtaining unique sequences is available at https://sourceforge.jp/projects/ parallelgwas/releases/