AAV inputs and parameters
Target tissue, serotype and payload limit for the literature lookup; a protein sequence for the optimizer. No species, route or promoter parameter exists.
The two AAV tools answer different questions and share only one parameter. aav_capsid_select is a literature lookup: you name a tissue and it returns what published studies reported for each serotype, with the model and citation per entry. aav_transgene_optimize is a codon optimizer: you give it a protein sequence and it reverse-translates and optimizes the coding sequence.
Capsid selection does not rank anything
There is no scoring, no ranking and no recommendation. The tool returns records and citations and leaves the judgement to you. Two consequences worth holding on to: a tissue no source reports is absent from the result rather than scored zero, so absence is missing evidence and not evidence of absence; and tropism reported in one species does not transfer to another, so read the model each entry was observed in before you carry a number across.
Capsid selection (aav_capsid_select)
target_tissuestringrequiredTissue to look up reported tropism for: cns, eye, heart, liver, lung or muscle. Aliases such as brain or retina are accepted and mapped.
serotype_preferencestringA specific serotype to return the full record for, e.g. AAV9 or AAV-PHP.eB. It does not promote that serotype in any ordering, because there is no ordering — it selects which record you get back in full.
max_payload_kbnumberdefault: 4.7Payload size in kb, checked against the ~4.7 kb AAV packaging limit (Wu et al., Mol Ther 2010;18:80-86). Omit it on the backend and no packaging verdict is returned at all; the tool sends 4.7 when you do not set it, so you get the verdict against the standard limit by default.
Transgene optimization (aav_transgene_optimize)
transgene_sequencestringrequiredThe protein sequence to reverse-translate and codon-optimize. This is an amino-acid sequence, not DNA — the tool produces the DNA. A trailing * stop codon is stripped, and whitespace is ignored.
⛔ DNA is not rejected, it is mis-read. Nothing validates this field, and A, C, G and T are all valid amino-acid letters, so a nucleotide sequence is reverse-translated as though it were a four-residue protein. The job succeeds, protein_length_aa comes back equal to your base count, and the optimized sequence is about three times the length you sent. Check protein_length_aa against the residue count you expected before trusting any run.
max_payload_kbnumberdefault: 4.7The same packaging check as above, applied to the optimized construct.
What the optimizer actually enforces
The run is DnaChisel with a fixed set of constraints, none of which you configure:
- Translation fidelity is enforced — the optimized DNA encodes your protein unchanged.
- GC content is held to 40–60% in a 60-nt sliding window.
- The common restriction sites
BsmBI,BsaI,EcoRIandBamHIare avoided. - Codon usage is optimized for Homo sapiens, and the codon table is fixed — there is no species parameter.
What these tools do not take
Nothing here designs an expression cassette. The backend optimizes the coding sequence only, so there is no parameter for a promoter, a polyadenylation signal, or regulatory elements such as WPRE, an intron or a Kozak sequence — and none is silently accepted either. Choose those yourself and assemble the cassette around the sequence this tool returns.
Capsid selection likewise takes no species, route of administration or neutralizing-antibody profile input. Species is reported per entry from the literature rather than requested, seroprevalence comes from the cited studies where one exists, and route is not modelled.
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AAV design on the platform
Select an AAV capsid serotype for a target tissue and optimize the transgene cassette for AAV packaging — the gene-therapy tools of the biologics cluster.
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.