getTrans {seqinr}R Documentation

Generic function to translate coding sequences into proteins

Description

This function translates nucleic acid sequences into the corresponding peptide sequence. It can translate in any of the 3 forward or three reverse sense frames. In the case of reverse sense, the reverse-complement of the sequence is taken. It can translate using the standard (universal) genetic code and also with non-standard codes. Ambiguous bases can also be handled.

Usage

getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
## S3 method for class 'SeqAcnucWeb':
getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = "auto", numcode = "auto")
## S3 method for class 'SeqFastadna':
getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = 0, numcode = 1)
## S3 method for class 'SeqFrag':
getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = 0, numcode = 1)

Arguments

object an object of the class SeqAcnucWeb or SeqFastadna, or SeqFrag or a list of these objects, or an object of class qaw created by query
numcode The ncbi genetic code number for translation. By default the standard genetic code is used, and for sequences coming from an ACNUC server the relevant genetic code is used by default.
NAstring How to translate amino-acids when there are ambiguous bases in codons.
ambiguous If TRUE, ambiguous bases are taken into account so that for instance GGN is translated to Gly in the standard genetic code.
frame Frame(s) (0,1,2) to translate. By default the frame 0 is used.
sens Direction for translation: F for the direct strand e and R for the reverse complementary strand.
... further arguments passed to or from other methods

Details

The following genetic codes are described here. The number preceding each code corresponds to numcode.

1
standard
2
vertebrate.mitochondrial
3
yeast.mitochondrial
4
protozoan.mitochondrial+mycoplasma
5
invertebrate.mitochondrial
6
ciliate+dasycladaceal
9
echinoderm+flatworm.mitochondrial
10
euplotid
11
bacterial+plantplastid
12
alternativeyeast
13
ascidian.mitochondrial
14
alternativeflatworm.mitochondrial
15
blepharism
16
chlorophycean.mitochondrial
21
trematode.mitochondrial
22
scenedesmus.mitochondrial
23
hraustochytrium.mitochondria

Value

For a single sequence an object of class character containing the characters of the sequence, either of length 1 when as.string is TRUE, or of the length of the sequence when as.string is FALSE. For many sequences, a list of these.

Author(s)

D. Charif and J.R. Lobry and L. Palmeira

References

citation("seqinr")

See Also

SeqAcnucWeb, SeqFastadna, SeqFrag\cr The genetic codes are given in the object \code{SEQINR.UTIL}, a more human readable form is given by the function \code{tablecode}. Use \code{aaa} to get the three-letter code for amino-acids.

Examples

#
# List all available methods for getTrans generic function:
#
   methods(getTrans)
#
# Toy CDS example invented by Leonor Palmeira:
#
  toycds <- s2c("tctgagcaaataaatcgg")
  getTrans(toycds) # should be c("S", "E", "Q", "I", "N", "R")
#
# Toy CDS example with ambiguous bases:
#
  toycds2 <- s2c("tcngarcarathaaycgn")
  getTrans(toycds2) # should be c("X", "X", "X", "X", "X", "X")
  getTrans(toycds2, ambiguous = TRUE) # should be c("S", "E", "Q", "I", "N", "R")
  getTrans(toycds2, ambiguous = TRUE, numcode = 2) # should be c("S", "E", "Q", "X", "N", "R")
#
# Real CDS example:
#
  realcds <- read.fasta(file = system.file("sequences/malM.fasta", package ="seqinr"))[[1]]
  getTrans(realcds)
# Biologically correct, only one stop codon at the end
  getTrans(realcds, frame = 3, sens = "R", numcode = 6)
# Biologically meaningless, note the in-frame stop codons

#
# Complex transsplicing operations, the correct frame and the correct 
# genetic code are automatically used for translation into protein for
# sequences coming from an ACNUC server:
#
## Not run: 
  # Need internet connection.
  # Translation of the following EMBL entry:
  #
  # FT   CDS             join(complement(153944..154157),complement(153727..153866),
  # FT                   complement(152185..153037),138523..138735,138795..138955)
  # FT                   /codon_start=1
  choosebank("emblTP")
  query("trans", "N=AE003734.PE35")
  getTrans(trans$req[[1]])
## End(Not run)

[Package seqinr version 1.1-6 Index]