CRISPR Guide Design

1. 01A whole build package: guides, off-targets, the repair template, the screening PCR, the protocol and the fragments to order
2. 02SpCas9 guide enumeration by PAM match on both strands
3. 03Origin-spanning guides on circular sequences, which a linear scan cannot find
4. 04Off-target search against a sequence you select as the search space, with mismatch tolerance
5. 05Guide composition readouts, including GC content and homopolymer runs
6. 06Guides written back to the map as annotations, so a chosen guide is visible in context
7. 07A repair template with homology arms and a PAM-disrupting mutation, silent where the cut falls in a coding sequence
8. 08Screening primers placed outside the homology arms, so the assay cannot amplify the donor instead of the locus

Guide search and off-target search are ports of cas-offinder and crisprScore, validated against golden vectors captured from those implementations. Scoring models still being sourced are tracked in docs/RESEARCH.md rather than approximated. The panel runs on @ports/crispr-screen, @ports/enzymes, @ports/guide, @ports/primer.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Does it find guides that cross the origin of a circular plasmid?

Yes. Circular sequences are searched as circular, so a guide whose protospacer wraps the origin is enumerated like any other.

What does it search for off-targets?

A sequence you choose as the search space, for example a genomic region loaded into the project. There is no remote genome query, because the search runs in the browser.