Use DNA Chisel Sequence Optimizer

Syntax Overview

Each line follows this format:
[,param1=value1[,param2=value2[,...]]]
Example:
AvoidPattern,pattern=GAATTC

🔒 AvoidChanges

Prevents edits in a specified sequence region.

Example:
AvoidChanges,location=100:150,max_edits=0 → Locks bases 100–150 from being modified.

🧬 AvoidHairpins

Blocks formation of hairpin secondary structures.

Example:
AvoidHairpins,stem_size=20,hairpin_window=200 → No hairpins with ≥20bp stems in any 200bp window.

🚫 AvoidPattern

Avoids a specific pattern from appearing in the DNA.

Example:
AvoidPattern,pattern=GAATTC → Avoids the EcoRI restriction site.

Advanced Example:
AvoidPattern,pattern=3x4mer,location=100:300,strand=0 → Avoids direct 4-mer repeats (3 times) in region 100–300 on both strands.

Pattern Matching Types (in matching order):
1. HomopolymerPattern: Repeats of same base, like 6xA or 9xC
2. RepeatedKmerPattern: Direct k-mer repeats, like 3x4mer
3. EnzymeSitePattern: Named restriction sites, e.g. BsmBI_site
4. DnaNotationPattern: Standard IUPAC codes, like ATGNNC
5. SequencePattern: Regex fallback, like G.{2}C

Additional parameters:
- location to restrict to a region
- strand = 1 (forward), -1 (reverse), 0 (both)

⚖️ EnforceGCContent

Constrains GC content within defined bounds.

Example (Constraint):
EnforceGCContent,mini=0.4,maxi=0.6,window=50
Example (Objective):
EnforceGCContent,target=0.5,boost=2.0,window=50

🌡 EnforceMeltingTemperature

Enforces melting temperature (Tm) range.

Example (Constraint): EnforceMeltingTemperature,mini=50,maxi=65,location=0:100 → Tm of region 0–100 must be 50–65°C.

Example (Objective): EnforceMeltingTemperature,target=55,boost=2.0,location=0:100 → Tm of region 0–100 should be close to 55°C.

🔄 EnforceTranslation

Ensures the DNA translates into a specific protein sequence.

Example:
EnforceTranslation,translation=MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGQK

🔧 CodonOptimize

Optimizes codons for a target species to improve expression (this objective should be used when EnforceTranslation is used).

Example (Objective):
CodonOptimize,species=e_coli → Uses codon table for E. coli.

🧬 Supported Species for Codon Optimization

Use these with species=:

• b_subtilis
  
• c_elegans
  
• d_melanogaster
  
• e_coli
  
• g_gallus
  
• h_sapiens
  
• m_musculus
  
• m_musculus_domesticus
  
• s_cerevisiae

Or use an NCBI TaxID.

For full documentation, visit the DNA Chisel GitHub repository.