Fig. 1
From: CRISPR-TE: a web-based tool to generate single guide RNAs targeting transposable elements
CRISPR-TE Workflow for Designing sgRNAs Targeting Transposable Elements. A Efficiently searches for all potential sgRNA target sites (N20NGG) using the Aho-Corasick algorithm on the genome FASTA file. B Employs a trie data structure to efficiently store sgRNA sequences, facilitating hamming distance mismatch searches. C Stores comprehensive sgRNA information for human and mouse genomes in a PostgreSQL database, consisting of two tables: the main table contains sgRNA sequences and coordinates, 6bp upstream and downstream sequences, on/off-target scores, genetic element classes, and the targeted TE (if applicable). D CRISPR-TE provides two approaches for sgRNA design targeting TEs: (i) targeting a single copy with minimal off-targets, and (ii) targeting a TE subfamily using optimal sgRNA combinations determined by a greedy algorithm