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BioSequenceTranslate[bioseq]

translates a DNA or RNA sequence bioseq to a peptide sequence.

BioSequenceTranslate[bioseq,gtt]

uses the genetic translation table gtt.

BioSequenceTranslate[bioseq,gtt,startspec]

treats start codons in bioseq according to the specification startspec.

Details
Details and Options Details and Options
Examples  
Basic Examples  
Scope  
Applications  
Possible Issues  
Neat Examples  
See Also
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History
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BioSequenceTranslate

BioSequenceTranslate[bioseq]

translates a DNA or RNA sequence bioseq to a peptide sequence.

BioSequenceTranslate[bioseq,gtt]

uses the genetic translation table gtt.

BioSequenceTranslate[bioseq,gtt,startspec]

treats start codons in bioseq according to the specification startspec.

Details

  • The genetic translation table gtt can be specified as follows:
  • Automaticthe standard code (default)
    "name"standard name of a "GeneticTranslationTable" entity
    Entity["GeneticTranslationTable",…]"GeneticTranslationTable" entity
    nNCBI genetic code number
    "AAAA…"length-64 NCBI codon translation string
    <|"cod1""tran1","cod2""tran2",…|>explicit codon translation table
  • The start codon specification startspec specifies what translation should be used for the first codon in bioseq. If no startspec is given, the first codon will be treated as a start codon only if bioseq can be identified as corresponding to a complete protein.
  • The following forms for startspec can be used to specific how to treat the first codon in bioseq:
  • Automatictreat as start codon only for complete proteins
    Falsenever treat as start codon
    Truealways treat as start code
  • The following additional forms for startspec can be used to define start codon behavior, overriding the specification implied by the genetic translation table gtt:
  • nuse NCBI genetic code number start codon specification
    "AAAA…"use length-64 NCBI start codon translation string
    <|"cod1""tran1","cod2""tran2",…|>explicit specify start codon translations

Examples

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Basic Examples  (1)

Translate a DNA sequence into the corresponding peptide sequences:

Wolfram Language code: BioSequenceTranslate[BioSequence["DNA", "CTGATATAC"]]

Scope  (8)

Translate an RNA sequence:

Wolfram Language code: BioSequenceTranslate[BioSequence["RNA", "CUGAUAUAC"]]

Translate using a "GeneticTranslationTable" entity:

Wolfram Language code: BioSequenceTranslate[BioSequence["DNA", "CTGATATAC"], Entity["GeneticTranslationTable", "VertebrateMitochondrial"]]

Translate using the table corresponding to a NCBI genetic code number:

Wolfram Language code: BioSequenceTranslate[BioSequence["DNA", "CTGATATAC"], 2]

Use an Association to specify the translation table:

Wolfram Language code: BioSequenceTranslate[BioSequence["DNA", "CTGATATAC"], <|"TTT" -> "F", "TTC" -> "F", "TTA" -> "L", "TTG" -> "L", "TCT" -> "S", "TCC" -> "S", "TCA" -> "S", "TCG" -> "S", "TAT" -> "Y", "TAC" -> "S", "TAA" -> "*", "TAG" -> "*", "TGT" -> "C", "TGC" -> "C", "TGA" -> "W", "TGG" -> "W", "CTT" -> "L", "CTC" -> "L", "CTA" -> "L", "CTG" -> "L", "CCT" -> "P", "CCC" -> "P", "CCA" -> "P", "CCG" -> "P", "CAT" -> "H", "CAC" -> "H", "CAA" -> "Q", "CAG" -> "Q", "CGT" -> "R", "CGC" -> "R", "CGA" -> "R", "CGG" -> "R", "ATT" -> "I", "ATC" -> "I", "ATA" -> "I", "ATG" -> "M", "ACT" -> "T", "ACC" -> "T", "ACA" -> "T", "ACG" -> "T", "AAT" -> "N", "AAC" -> "N", "AAA" -> "K", "AAG" -> "K", "AGT" -> "S", "AGC" -> "S", "AGA" -> "*", "AGG" -> "*", "GTT" -> "V", "GTC" -> "V", "GTA" -> "V", "GTG" -> "V", "GCT" -> "A", "GCC" -> "A", "GCA" -> "A", "GCG" -> "A", "GAT" -> "D", "GAC" -> "D", "GAA" -> "E", "GAG" -> "E", "GGT" -> "G", "GGC" -> "G", "GGA" -> "G", "GGG" -> "G"|>]

Use an arbitrary NCBI translation table:

Wolfram Language code: BioSequenceTranslate[BioSequence["DNA", "CTGATATAC"], "GGGGEEDDAAAAVVVVRRSSKKNNTTTTMIIIRRRRQQHHPPPPLLLLW*CC**YYSSSSLLFF"]

Use the start translation of the automatically selected translation table:

Wolfram Language code: BioSequenceTranslate[BioSequence["CTGATATAC"], Automatic, True]

Specify start codon translations with an association of the changed start codons:

Wolfram Language code: BioSequenceTranslate[BioSequence["DNA", "CTGATATAC"], Automatic, <|"CTG" -> "R"|>]

Use NCBI notation to specify the start codon translation:

Wolfram Language code: BioSequenceTranslate[BioSequence["DNA", "CTGATATAG"], Automatic, "GGGGEEDDAAAAVVVVRRSSKKNNTTTTMIIIRRRRQQHHPPPPLLLLW*CC**YYSSSSLLFF"]

Applications  (2)

The translations to selenocysteine (U) and pyrrolysine (O) only happen in particular chemical contexts that are distinct from the translation system for a particular organism. One way to incorporate them is to change the codon translation association:

Wolfram Language code: standardTranslations = Entity["GeneticTranslationTable", "Standard"]["CodonTranslations"]; BioSequenceTranslate[BioSequence["DNA", "GGCTGATAGTAA"], AssociateTo[standardTranslations, specialRules = {"TGA" -> "U", "TAG" -> "O"}]]

After splicing together coding sequences, translation yields the same sequence as the protein:

Wolfram Language code: hbbBioSeq = BioSequence[Interpreter["Gene"]["human hbb gene"]]; spliced = StringJoin@@StringTake[hbbBioSeq, {{51, 142}, {273, 495}, {1346, 1474}}]; translated = BioSequenceModify[BioSequenceTranslate[spliced, Automatic, True], "DropFromStopLetter"]
Wolfram Language code: targetProtein = BioSequence[Interpreter["Protein"]["hbb"]]
Wolfram Language code: SequenceAlignment[targetProtein, translated]

Possible Issues  (2)

Inputs with degenerate letters may have multiple possible translations with no single generalization:

Wolfram Language code: BioSequenceTranslate[BioSequence["RNA", "SUGAUAUAC"]]

Using BioSequenceInstances first will avoid ambiguous results:

Wolfram Language code: BioSequenceTranslate /@ BioSequenceInstances[BioSequence["RNA", "SUGAUAUAC"]]

If the length of a DNA or RNA sequence is not a multiple of three, then the remaining letters after constructing codons are discarded from the end of the sequence:

Wolfram Language code: BioSequenceTranslate[BioSequence["DNA", "CTGATATACGG"]]

Neat Examples  (2)

See the peptides resulting from translation:

Wolfram Language code: acgt = {"A", "C", "G", "T"}; Graphics3D[Table[aa = BioSequenceTranslate[dna = BioSequence["DNA", StringJoin[acgt[[{i1, i2, i3}]]]]]; mol = If[aa =!= BioSequence["Peptide", "."], Molecule[aa], Null]; molpl = If[aa =!= BioSequence["Peptide", "."], MoleculePlot3D[mol], "STOP"]; Inset[Tooltip[Rasterize[molpl, ImageSize -> 40, Background -> None], Column[{CommonName[Entity["BioSequenceType", "Peptide"]["AlphabetRules"][aa["SequenceString"]]]//Quiet, aa, mol, dna}]], {i1, i2, i3}], {i1, 4}, {i2, 4}, {i3, 4}], Boxed -> False, Axes -> True, AxesOrigin -> {0, 0, 0}, Ticks -> Table[Transpose[{Range[4], Style[#, Bold]& /@ acgt}], {3}]]

Reveal a phrase encoded in DNA:

Wolfram Language code: BioSequenceTranslate[BioSequence["DNA", "GGAGAAAACGAAACAATATGCAGC"]]
Wolfram Research (2020), BioSequenceTranslate, Wolfram Language function, https://reference.wolfram.com/language/ref/BioSequenceTranslate.html.

Text

Wolfram Research (2020), BioSequenceTranslate, Wolfram Language function, https://reference.wolfram.com/language/ref/BioSequenceTranslate.html.

CMS

Wolfram Language. 2020. "BioSequenceTranslate." Wolfram Language & System Documentation Center. Wolfram Research. https://reference.wolfram.com/language/ref/BioSequenceTranslate.html.

APA

Wolfram Language. (2020). BioSequenceTranslate. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/BioSequenceTranslate.html

BibTeX

@misc{reference.wolfram_2026_biosequencetranslate, author="Wolfram Research", title="{BioSequenceTranslate}", year="2020", howpublished="\url{https://reference.wolfram.com/language/ref/BioSequenceTranslate.html}", note=[Accessed: 12-June-2026]}

BibLaTeX

@online{reference.wolfram_2026_biosequencetranslate, organization={Wolfram Research}, title={BioSequenceTranslate}, year={2020}, url={https://reference.wolfram.com/language/ref/BioSequenceTranslate.html}, note=[Accessed: 12-June-2026]}