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SynDesign is a web-based tool designed for the creation of prime editing guide RNAs (pegRNAs). It offers a comprehensive solution for pegRNA design, evaluation, and library construction for saturation genome editing (SGE). The tool accommodates various gene identification inputs, including gene symbols and identifiers from popular databases such as RefSeq (NM IDs), Ensembl, and HGNC IDs, as well as user-provided FASTA sequences.
Users have the flexibility to target individual exons within the coding sequence of each gene or perform a comprehensive evaluation of the entire gene. It is important to note that for larger genes, a complete gene evaluation may require several hours or possibly days to finish.
SynDesign also supports additional input formats, including allele and mutation IDs sourced from the ClinVar and COSMIC databases, respectively. Users can also leverage sequence and genomic position-based queries for simpler runs.
The evaluation process relies on DeepPrime, a prime editing efficiency prediction tool based on deep learning. Developed to forecast pegRNA efficiency across various prime editors and cell types, DeepPrime is adept at predicting outcomes for substitutions, insertions, and deletions up to 3 base pairs in size. It also considers primer binding site (PBS) lengths spanning 1 to 17 base pairs, reverse transcription template (RTT) lengths ranging from 1 to 40 base pairs, and edit positions from +1 to +30. For more details on DeepPrime and its methodology, please refer to Yu et al., Cell 2023.
COSMIC. COSMIC is a product of Genome Research Limited (Wellcome Sanger Institute). It is free for academic and non-commercial use; commercial use requires a COSMIC licence. Lookups here resolve a single user-typed identifier — no COSMIC data is listed, browsable or served in bulk.
epegRNA. The engineered pegRNA (epegRNA) 3' motifs (tevopreQ1, tevo2.0 and the related v2 motifs) are the subject of a Broad Institute patent application; commercial users may need a licence to use them.
If you have any questions, bug reports, or suggestions, please do not hesitate to contact us through the Support page.