translate: Translate nucleic acid sequences into proteins
In seqinr: Biological Sequences Retrieval and Analysis

translate

R Documentation

Translate nucleic acid 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

translate(seq, frame = 0, sens = "F", numcode = 1, NAstring = "X", ambiguous = FALSE)

Arguments

`seq`	the sequence to translate as a vector of single characters in lower case letters.
`frame`	Frame(s) (0,1,2) to translate. By default the frame `0` is used.
`sens`	Sense to translate: `F` for forward sense and `R` for reverse sense.
`numcode`	The ncbi genetic code number for translation. By default the standard genetic code is used.
`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.

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: thraustochytrium.mitochondria
24: Pterobranchia.mitochondrial
25: CandidateDivision.SR1+Gracilibacteria
26: Pachysolen.tannophilus

Value

translate returns a vector of single characters containing the peptide sequence in the standard one-letter IUPAC code. Termination (STOP) codons are translated by the character '*'.

Author(s)

D. Charif, J.R. Lobry

References

The genetic codes have been taken from the ncbi taxonomy database: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi. Last update October 05, 2000.
The IUPAC one-letter code for aminoacids is described at: https://www.bioinformatics.org/sms/iupac.html

citation("seqinr")

Examples

##
## Toy CDS example invented by Leonor Palmeira:
##
toycds <- s2c("tctgagcaaataaatcgg")
translate(seq = toycds) # should be c("S", "E", "Q", "I", "N", "R")
##
## Toy CDS example with ambiguous bases:
##
toycds2 <- s2c("tcngarcarathaaycgn")
translate(toycds2) # should be c("X", "X", "X", "X", "X", "X")
translate(toycds2, ambiguous = TRUE) # should be c("S", "E", "Q", "I", "N", "R")
translate(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]]
translate(seq = realcds)
# Biologically correct, only one stop codon at the end
translate(seq = 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)

## 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
## FT                   /db_xref="FLYBASE:FBgn0002781"
## FT                   /db_xref="GOA:Q86B86"
## FT                   /db_xref="TrEMBL:Q86B86"
## FT                   /note="mod(mdg4) gene product from transcript CG32491-RZ;
## FT                   trans splicing"
## FT                   /gene="mod(mdg4)"
## FT                   /product="CG32491-PZ"
## FT                   /locus_tag="CG32491"
## FT                   /protein_id="AAO41581.1"
## FT                   /translation="MADDEQFSLCWNNFNTNLSAGFHESLCRGDLVDVSLAAEGQIVKA
## FT                   HRLVLSVCSPFFRKMFTQMPSNTHAIVFLNNVSHSALKDLIQFMYCGEVNVKQDALPAF
## FT                   ISTAESLQIKGLTDNDPAPQPPQESSPPPAAPHVQQQQIPAQRVQRQQPRASARYKIET
## FT                   VDDGLGDEKQSTTQIVIQTTAAPQATIVQQQQPQQAAQQIQSQQLQTGTTTTATLVSTN
## FT                   KRSAQRSSLTPASSSAGVKRSKTSTSANVMDPLDSTTETGATTTAQLVPQQITVQTSVV
## FT                   SAAEAKLHQQSPQQVRQEEAEYIDLPMELPTKSEPDYSEDHGDAAGDAEGTYVEDDTYG
## FT                   DMRYDDSYFTENEDAGNQTAANTSGGGVTATTSKAVVKQQSQNYSESSFVDTSGDQGNT
## FT                   EAQVTQHVRNCGPQMFLISRKGGTLLTINNFVYRSNLKFFGKSNNILYWECVQNRSVKC
## FT                   RSRLKTIGDDLYVTNDVHNHMGDNKRIEAAKAAGMLIHKKLSSLTAADKIQGSWKMDTE
## FT                   GNPDHLPKM"
choosebank("emblTP")
trans <- query("trans", "N=AE003734.PE35")
trans1 <- getTrans(trans$req[[1]])
## Complex transsplicing operations, the correct frame and the correct
## genetic code are automatically used for translation into protein.
seq <- getSequence(trans$req[[1]])
identical(translate(seq),trans1)
#default frame and genetic code are correct
trans <- query("trans", "N=AB004237")
trans1 <- getTrans(trans$req[[1]])
## Complex transsplicing operations, the correct frame and the correct
## genetic code are automatically used for translation into protein.
seq <- getSequence(trans$req[[1]])
identical(translate(seq),trans1)
#default  genetic code is not correct
identical(translate(seq,numcode=2),trans1)
#genetic code is 2

## End(Not run)

seqinr documentation built on May 29, 2024, 6:36 a.m.