Data Visualization of CRISPR-Cas9 Guide RNA Design Tools.

With the advancement of genomic engineering and genetic modification techniques, the uptake of computational tools to design guide RNA increased drastically. Searching for genomic targets to design guides with maximum on-target activity (efficiency) and minimum off-target activity (specificity) is now an essential part of genome editing experiments. Today, a variety of tools exist that allow the search of genomic targets and let users customize their search parameters to better suit their experiments. Here we present an overview of different ways to visualize these searched CRISPR target sites along with specific downstream information like primer design, restriction enzyme activity and mutational outcome prediction after a double-stranded break. We discuss the importance of a good visualization summary to interpret information along with different ways to represent similar information effectively.

Synsor: a tool for alignment-free detection of engineered DNA sequences.

DNA sequences of nearly any desired composition, length, and function can be synthesized to alter the biology of an organism for purposes ranging from the bioproduction of therapeutic compounds to invasive pest control. Yet despite offering many great benefits, engineered DNA poses a risk due to their possible misuse or abuse by malicious actors, or their unintentional introduction into the environment. Monitoring the presence of engineered DNA in biological or environmental systems is therefore crucial for routine and timely detection of emerging biological threats, and for improving public acceptance of genetic technologies. To address this, we developed Synsor, a tool for identifying engineered DNA sequences in high-throughput sequencing data. Synsor leverages the k-mer signature differences between naturally occurring and engineered DNA sequences and uses an artificial neural network to classify whether a DNA sequence is natural or engineered. By querying suspected sequences against the model, Synsor can identify sequences that are likely to have been engineered. Using natural plasmid and engineered vector sequences, we showed that Synsor identifies engineered DNA with >99% accuracy. We demonstrate how Synsor can be used to detect potential genetically engineered organisms and locate where engineered DNA is being introduced into the environment by analysing genomic and metagenomic data from yeast and wastewater samples, respectively. Synsor is therefore a powerful tool that will streamline the process of identifying engineered DNA in poorly characterized biological or environmental systems, thereby allowing for enhanced monitoring of emerging biological threats.