DNA Chisel Sequence Optimizer
DnaChisel edits DNA sequences to satisfy biological constraints and optimize properties like codon usage, motif distribution, and GC content.
DnaChisel is a tool for optimizing DNA sequences by satisfying biological constraints and enhancing desirable properties. It applies a two-stage strategy: first resolving constraint violations (such as avoiding specific motifs, enforcing translation fidelity, or maintaining GC content), then maximizing objectives like codon adaptation or minimizing undesired patterns. Its mutation-space search allows efficient editing while supporting multiple optimization goals simultaneously. DnaChisel has been applied to tasks such as codon optimization, elimination of restriction sites, and GC balancing, with customizable rules for a wide range of use cases.
Estimated resource cost: 0.000062
Categories: Sequence Analysis & Annotation
Tags: Codon Optimization Expression
Key Capabilities
- Defines DNA optimization problems using a human-readable, constraint-based DSL.
- Separates hard constraints from soft objectives to ensure valid yet optimal sequences.
- Supports dozens of built-in specifications, including GC content, codon usage, and restriction sites.
- Allows precise control over editable regions, locked sequences, and biological constraints like translation and melting temperature.
- Optimizes sequences using a modular engine that supports constraints solving, random mutations, and exhaustive search strategies.
Runtime Statistics
| Metric | Value |
|---|---|
| runtime_mean | 10 |
| runtime_median | 10 |
| runtime_std | 4 |
| runtime_90th_percentile | 17 |
| runtime_max | 23 |
Similar Tools
- CodonTransformer
- TIsigner Expression Optimization
- ANARCI
- ANARCII
Ready to submit your job?
Review your configuration, then confirm the estimated credit cost before you run the job. Note that credit estimates are not guaranteed and runtime can vary depending on inputs and settings.
Estimated Credits: 0.000062
Invite-only, limited-time access. Please contact ztang@getantibody.com.
Invite-only, limited-time access. Please contact ztang@getantibody.com.