eDNAfuns (version 0.1.0)

count_stop_codons: Count stop codons or return translated sequence

Description

Given a DNA sequence (either a `DNAString` object or a character string), this function translates it using a specified genetic code and counts the number of stop codons (`*`) in the resulting amino acid sequence. Alternatively, the translated sequence itself can be returned.

Usage

count_stop_codons(
  sequence = NULL,
  format = "DNAString",
  codon = 1,
  dictionary = 5,
  return = "count"
)

Value

If `return = "count"`, an integer giving the number of stop codons. Otherwise, a character string with the translated amino acid sequence.

Arguments

sequence

A DNA sequence, either as a [Biostrings::DNAString] object or as a character string.

format

Input format, either `"DNAString"` (default) or `"character"`. If `"character"`, the sequence must consist of `A`, `C`, `G`, `T` only.

codon

Integer giving the starting codon position (usually 1, 2, or 3).

dictionary

Integer specifying which translation code to use. See [Biostrings::GENETIC_CODE_TABLE] for all options. Common examples:

id	name
1	Standard
2	Vertebrate Mitochondrial
3	Yeast Mitochondrial
4	Mold/Protozoan/Coelenterate/Mycoplasma/Spiroplasma Mitochondrial
5	Invertebrate Mitochondrial
6	Ciliate/Dasycladacean/Hexamita Nuclear
9	Echinoderm/Flatworm Mitochondrial
10	Euplotid Nuclear
11	Bacterial, Archaeal, and Plant Plastid
12	Alternative Yeast Nuclear
13	Ascidian Mitochondrial
14	Alternative Flatworm Mitochondrial
15	Blepharisma Macronuclear
16	Chlorophycean Mitochondrial
21	Trematode Mitochondrial
22	Scenedesmus obliquus Mitochondrial
23	Thraustochytrium Mitochondrial
24	Pterobranchia Mitochondrial
25	Candidate Division SR1 and Gracilibacteria
26	Pachysolen tannophilus Nuclear

return

Either `"count"` (default) to return the number of stop codons, or any other value to return the translated amino acid sequence.

Author

Ramon Gallego, 2021

Details

The function uses [Biostrings::translate()] with the specified starting position and genetic code. Translation warnings are suppressed.

Examples

if (requireNamespace("Biostrings", quietly = TRUE)) {
  library(Biostrings)
  seq <- DNAString("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG")
  count_stop_codons(seq, codon = 1, dictionary = 1)
  count_stop_codons(seq, codon = 1, dictionary = 1, return = "translation")
}