seq_translate

Translate DNA/RNA sequences into amino acids

Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences).
Implements S3 infrastructure to work with biological sequences as described in Keck (2020) <doi:10.1111/2041-210X.13490>.
Provides a collection of functions to perform biological conversion among classes
(transcription, translation) and basic operations on sequences
(detection, selection and replacement based on positions or patterns).
The package also provides functions to import and export sequences from and to other package formats.

Francois Keck

bioseq

A Toolbox for Manipulating Biological Sequences

seq_translate function

<dl><dt>x</dt>
<dd>a vector of DNA (bioseq_dna) or RNA (bioseq_rna).</dd>
<dt>code</dt>
<dd>an integer indicating the genetic code to use for translation
(default 1 uses the Standard genetic code). See Details.</dd>
<dt>codon_frame</dt>
<dd>an integer giving the nucleotide position
where to start translation.</dd>
<dt>codon_init</dt>
<dd>a logical indicating whether the first codon is evaluated
as a possible codon start and translated to methionine.</dd></dl>

Arguments

Translate DNA/RNA sequences into amino acids — seq_translate

<dl>

<dt>x</dt>
<dd>a vector of DNA (bioseq_dna) or RNA (bioseq_rna).</dd>


<dt>code</dt>
<dd>an integer indicating the genetic code to use for translation
(default 1 uses the Standard genetic code). See Details.</dd>


<dt>codon_frame</dt>
<dd>an integer giving the nucleotide position
where to start translation.</dd>


<dt>codon_init</dt>
<dd>a logical indicating whether the first codon is evaluated
as a possible codon start and translated to methionine.</dd>

</dl>

seq_translate: Translate DNA/RNA sequences into amino acids

Description

Usage

Value

Arguments

Details

See Also

Examples