translate {Biostrings}R Documentation

DNA/RNA transcription and translation

Description

Functions for transcription and/or translation of DNA or RNA sequences, and related utilities.

Usage

## Transcription:
transcribe(x)
cDNA(x)

## Translation:
codons(x)
translate(x)

## Related utilities:
dna2rna(x)
rna2dna(x)

Arguments

x A DNAString object for transcribe and dna2rna.

An RNAString object for cDNA and rna2dna.

A DNAString, RNAString, MaskedDNAString or MaskedRNAString object for codons.

A DNAString, RNAString, DNAStringSet, RNAStringSet, MaskedDNAString or MaskedRNAString object for translate.

Details

transcribe reproduces the biological process of DNA transcription that occurs in the cell. It takes the naive approach to treat the whole sequence x as if it was a single exon. See extractTranscripts for a more powerful version that allows the user to extract a set of transcripts specified by the starts and ends of their exons as well as the strand from which the transcript is coming.

cDNA reproduces the process of synthesizing complementary DNA from a mature mRNA template.

translate reproduces the biological process of RNA translation that occurs in the cell. The input of the function can be either RNA or coding DNA. The Standard Genetic Code (see ?GENETIC_CODE) is used to translate codons into amino acids. codons is a utility for extracting the codons involved in this translation without translating them.

dna2rna and rna2dna are low-level utilities for converting sequences from DNA to RNA and vice-versa. All what this converstion does is to replace each occurrence of T by a U and vice-versa.

Value

An RNAString object for transcribe and dna2rna.

A DNAString object for cDNA and rna2dna.

Note that if the sequence passed to transcribe or cDNA is considered to be oriented 5'-3', then the returned sequence is oriented 3'-5'.

An XStringViews object with 1 view per codon for codons. When x is a MaskedDNAString or MaskedRNAString object, its masked parts are interpreted as introns and filled with the + letter in the returned object. Therefore codons that span across masked regions are represented by views that have a width > 3 and contain the + letter. Note that each view is guaranteed to contain exactly 3 base letters.

An AAString object for translate.

See Also

reverseComplement, GENETIC_CODE, DNAString-class, RNAString-class, AAString-class, XStringSet-class, XStringViews-class, MaskedXString-class

Examples

  file <- system.file("extdata", "someORF.fa", package="Biostrings")
  x <- read.DNAStringSet(file)
  x

  ## The first and last 1000 nucleotides are not part of the ORFs:
  x <- DNAStringSet(x, start=1001, end=-1001)

  ## Before calling translate() on an ORF, we need to mask the introns
  ## if any. We can get this information fron the SGD database
  ## (http://www.yeastgenome.org/).
  ## According to SGD, the 1st ORF (YAL001C) has an intron at 71..160
  ## (see http://db.yeastgenome.org/cgi-bin/locus.pl?locus=YAL001C)
  y1 <- x[[1]]
  mask1 <- Mask(length(y1), start=71, end=160)
  masks(y1) <- mask1
  y1
  translate(y1)

  ## Codons
  codons(y1)
  which(width(codons(y1)) != 3)
  codons(y1)[20:28]

[Package Biostrings version 2.20.1 Index]