BioSequenceBackTranslateList

BioSequenceBackTranslateList[bioseq]

gives the generalized back translations of a peptide sequence bioseq.

BioSequenceBackTranslateList[bioseq,gtt]

uses the genetic translation table gtt.

BioSequenceBackTranslateList[bioseq,gtt,startspec]

treats the starting amino acid in bioseq according to the specification startspec.

Details and Options

  • BioSequenceBackTranslateList will use degenerate letters to minimize the size of the returned list.
  • 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 amino acid translation string
    <|"cod1""tran1","cod2""tran2",…|>explicit coding translation table
  • The start codon specification startspec specifies what translation should be used for the first amino acid in bioseq. If no startspec is given, the first amino acid will be treated as a starting acid only if bioseq is a protein entity or some other specification of a complete protein.
  • The following forms for startspec can be used to specify how to treat the first amino acid in bioseq:
  • Automaticuse a start translation only for complete proteins
    Falsenever use a start translation
    Truealways use a start translation
  • 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
  • BioSequenceBackTranslateList takes the following option:
  • MaxItems 10000maximum number of result sequences

Examples

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Basic Examples  (1)

Find a generalized back translation of a peptide sequence:

Obtain several back translations when the result cannot be expressed as a single degenerate sequence:

Scope  (6)

Back translate using a "GeneticTranslationTable" entity:

Use an Association to specify the translation table:

Use an arbitrary NCBI translation table:

Use the start translation of the automatically selected translation table:

Observe the difference of not using a start translation:

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

Use NCBI notation to specify the start codon translation:

Options  (1)

MaxItems  (1)

Choose the maximum number of items returned by the translation:

The default number of translation results is capped:

Infinity allows all possible back translations:

Properties & Relations  (1)

BioSequenceBackTranslateList returns a small number of degenerate sequences:

Map BioSequenceInstances across the result to obtain concrete sequences:

Neat Examples  (1)

Encode a phrase in DNA:

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

Text

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

CMS

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

APA

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

BibTeX

@misc{reference.wolfram_2023_biosequencebacktranslatelist, author="Wolfram Research", title="{BioSequenceBackTranslateList}", year="2020", howpublished="\url{https://reference.wolfram.com/language/ref/BioSequenceBackTranslateList.html}", note=[Accessed: 19-April-2024 ]}

BibLaTeX

@online{reference.wolfram_2023_biosequencebacktranslatelist, organization={Wolfram Research}, title={BioSequenceBackTranslateList}, year={2020}, url={https://reference.wolfram.com/language/ref/BioSequenceBackTranslateList.html}, note=[Accessed: 19-April-2024 ]}