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How to Get Started

1) Start with your CDS

What you do: Paste or upload the coding sequence (start → stop) you want to optimize.

Validators run automatically:

  • Length multiple of 3
  • Start/stop detection
  • Illegal characters
  • Internal stop codons

Recommended metadata: project name, organism/host, target tissue or cell type (optional), notes.

=== "Paste (single)"
Paste your CDS (DNA alphabet). RNA U will be converted to T with a confirmation step.

2) Set design objectives

What you do: Choose optimization targets and constraints. Subscription tier may cap how many objectives you can run at once, the number of sequences generated per job, and the number of jobs you can run per month.

Optimization Objectives: AutoNA enables you to optimize for multiple objectives at once.

  • Translation & Expression: translation efficiency in human cells
  • Stability & Durability: half-life in human cells
  • Protein Production: protein abundance in human cells
Tip "Balancing trade-offs"

Hover any objective to see how it’s scored and how it trades off with others. Always start with a single objective and incrementally add additional objectives to explore trade-offs.

3) Generate design candidates

What happens: AutoNA synthesizes candidates and scores them with interpretable plots.

You’ll see:

  • Run panel: queue position, compute estimate
  • Candidates table: ID · overall score · constraint status · notable motifs · delta vs baseline
  • Plot gallery:
    • Multi-objective Pareto front (hover for candidate details)
    • MFE/structure profile (windowed)
    • Immunogenicity motif density
    • GC distribution & repeat runs

Candidate details drawer

  • Full sequence with diff highlights vs input
  • 5′/3′ UTR designs (if generated) with motif annotations
  • Metric scores (depending on your optimization objective)
  • Metric fold changes compared to human alpha-globin UTR baseline with input ORF
  • Predicted minimum free energy in 5'/3' UTRs
  • Distance to first stem in the predicted secondary structure
  • GC content
  • Consistency (Validator that verifies designed CDS translates into intended amino acid sequence)
  • Download Seq list (CSV or Excel)

4) Compare & export

What you do: Select finalists, review summaries & benchmarks, then export for downstream experiments.

Comparison board (up to 4 side-by-side)

  • Radar charts · score tables · constraint satisfaction
  • Benchmark against your original CDS and (optionally) a public baseline

Export options

  • FASTA / CSV (sequences + metadata)
  • Annotated GenBank (if UTRs included)
  • PDF report (plots + rationale)

Tips for best results

  • Match host context: scores are host-aware; choose the correct organism
  • Balance objectives: avoid too many objectives in one run
  • Use constraints sparingly: hard constraints can significantly shrink the search space
  • Pin & annotate: capture rationale for team review and audits