Generic function to translate coding sequences into proteins
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.
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)
object |
an object of the class |
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 |
sens |
Direction for translation: |
... |
further arguments passed to or from other methods |
The following genetic codes are described here. The number preceding each code
corresponds to numcode.
standard
vertebrate.mitochondrial
yeast.mitochondrial
protozoan.mitochondrial+mycoplasma
invertebrate.mitochondrial
ciliate+dasycladaceal
echinoderm+flatworm.mitochondrial
euplotid
bacterial+plantplastid
alternativeyeast
ascidian.mitochondrial
alternativeflatworm.mitochondrial
blepharism
chlorophycean.mitochondrial
trematode.mitochondrial
scenedesmus.mitochondrial
hraustochytrium.mitochondria
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.
D. Charif, J.R. Lobry, L. Palmeira
citation("seqinr")
SeqAcnucWeb, SeqFastadna, SeqFrag
The genetic codes are given in the object SEQINR.UTIL, a more
human readable form is given by the function tablecode.
Use aaa to get the three-letter code for amino-acids.
#
# 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
# Read from an alignment as suggested by Dr. H. Suzuki
fasta.res <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"),
format = "fasta")
AA1 <- seqinr::getTrans(s2c(fasta.res$seq[[1]]))
AA2 <- seqinr::translate(s2c(fasta.res$seq[[1]]))
identical(AA1, AA2)
AA1 <- lapply(fasta.res$seq, function(x) seqinr::getTrans(s2c(x)))
AA2 <- lapply(fasta.res$seq, function(x) seqinr::translate(s2c(x)))
identical(AA1, AA2)
#
# 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")
trans <- query("trans", "N=AE003734.PE35")
getTrans(trans$req[[1]])
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