Genome editing and bioinformatics
Kazuki Nakamae, Hidemasa Bono
Abstract
Bioinformatics has become an indispensable technology in molecular biology for genome editing. In this review, we outline various bioinformatic techniques necessary for genome editing research. We first review state-of-the-art computational tools developed for genome editing studies. We then introduce a bio-digital transformation (BioDX) approach, which fully utilizes existing databases for biological innovation, and uses publicly available bibliographic full-text data and transcriptome data to survey genome editing target genes in model organism species, where substantial genomic information and annotation are readily available. We also discuss genome editing attempts in species with almost no genomic information. The transcriptome data, sequenced genomes, and functional annotations for these species are described, with a primary focus on the bioinformatic tools used for these analyses. Finally, we conclude on the need to maintain a database of genome editing resources for future development of genome editing research. Our review shows that the integration and maintenance of useful resources remains a challenge for bioinformatics research in genome editing, and that it is crucial for the research community to work together to create and maintain such databases in the future.