AAV quickstart
Name a target tissue for per-serotype tropism reports with citations and no ranking, then codon-optimize a protein transgene against the 4.7 kb limit.
You are designing an AAV gene therapy and you need two things: a capsid that reaches your target tissue, and a transgene cassette that fits inside it. The AAV tools do both in order — rank capsids for the tissue, then codon-optimize the transgene and check it against the packaging limit.
Select a capsid
Name the target tissue
Give the tissue you want to transduce: cns, eye, heart, liver, lung or muscle. Aliases such as brain or retina are accepted. This is the one required input.
Narrow to one serotype, optionally
Set serotype_preference to get that serotype's full record back, and max_payload_kb to have your payload checked against the ~4.7 kb packaging limit. A serotype name that is not in the reference table is rejected with the list of known names, so a typo fails loudly rather than returning nothing.
There is no species, route-of-administration or neutralizing-antibody input. Species is reported per observation from the literature rather than requested.
Read the reports, because nothing ranks them
Capsid selection runs as an asynchronous Modal job. It returns, per serotype, the tissues a cited study reports, the level that study reports, the species it was observed in, and the citation — in alphabetical order, with no score and no recommendation.
Two things to check before you shortlist anything: the model on each observation, since a high reported in mice is not a claim about humans; and whether a tissue is absent rather than low, because a tissue no source reports simply does not appear.
Optimize the transgene
Provide the transgene
Paste the protein sequence to optimize — an amino-acid sequence. The tool reverse-translates it, so the DNA is the output, not the input. A trailing * stop is stripped for you, and whitespace is ignored.
⛔ Do not paste DNA here. Nothing validates the input, and A, C, G and T are all valid amino-acid letters, so a nucleotide sequence is silently reverse-translated as if it were a four-residue protein. You get a successful job, a sequence roughly three times the length you sent, and a protein_length_aa equal to your DNA's base count. There is no error to warn you.
Set the payload limit
Set the maximum payload size (default 4.7 kb). It is the only other input this tool takes, and it only decides whether a packaging verdict comes back.
Everything else about the run is fixed and not configurable: codon usage is optimized for Homo sapiens with no species parameter, GC content is held to 40–60% in a 60-nt window, translation fidelity is enforced, and BsmBI, BsaI, EcoRI and BamHI are avoided. There is no promoter, polyadenylation or regulatory-element input — the backend optimizes the coding sequence only and does not design a cassette, so assemble those around the sequence it returns.
Submit and read feasibility
Transgene optimization runs as an asynchronous GPU job on Modal. The result card shows the optimized sequence, its length in kb, GC content, codon-optimization score, and whether it fits the AAV packaging limit.
In chat
Describe the gene therapy and the model runs both steps in order.
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AAV outputs and interpretation
Published tropism reports per serotype — tissue, level, model, citation — in alphabetical order with no score, plus the aav_packaging_feasible go/no-go.
Genomics & Multi-Omics overview
Cluster and annotate single-cell RNA-seq, find differentially expressed genes, map pathway enrichment, and get from a disease signal to a druggable target.