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— Entry 005 · 2026.09.19 —

CRISPR Design — design sgRNA and homology arms for a target gene in your chassis

Pick a chassis and a target gene; get ranked sgRNA candidates with PAM, activity score, and off-target risk, plus left/right homology arms.

Home/Tools/CRISPR Design
01

How it works

From a chassis and a target site to a complete CRISPR editing plan, five stages annotate each step in this entry.

  1. 01

    Select chassis

    Choose from a 30-strain chassis library spanning bacteria, yeast, and filamentous fungi.

  2. 02

    Select target site

    Find a gene by name or keyword, list repeat elements, or paste a bare DNA sequence.

  3. 03

    sgRNA design

    Scan for PAM, score on-target activity, and rank off-target risk per candidate.

  4. 04

    Homology arm design

    Build left/right arms with copy-number and PAM-disruption checks.

  5. 05

    Export

    Copy sgRNA ordering format and download homology-arm FASTA.

02

What it does

30-strain chassis library

Bacteria, yeast, and filamentous fungi, each with strain-specific genome annotations.

Activity scoring & off-target

Rank guides by Azimuth score and flag MM0/MM1/MM2+ off-target hits.

PAM disruption

Synonymous-mutate PAM sites inside the arms to prevent Cas9 re-cutting.

Species-specific arm length

Default and recommended homology-arm lengths tuned per chassis.

CRISPRsgRNAhomology armPAMoff-targetgene knockout
03

Input

Pick a chassis, name a target gene (or paste a sequence), then design.

The host organism to edit. Strains without genome annotation fall back to a reference strain.

Standard name, systematic name, locus tag, or function keyword.

When set, this is used instead of the gene search. Gene mode also designs homology arms.

These apply to homology-arm design in gene mode.

Runs against the live engine.
04

Design progress

Watch the design advance stage by stage.

Waiting for input
    05

    Result

    The ranked sgRNA candidates and the left/right homology arms with copy-number and PAM-disruption notes.

    06

    Workspace

    Save this run to your workspace

    Each saved run becomes a reproducible entry with an Entry ID you can cite in your methods. Handoff to the Expression Cassette Designer prefills the guide sequence.

    Run the design first, then save it here.