translate: Translate nucleic acid sequences

Description

This function translates nucleic acid sequences to 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 a selection of non-standard codes.

Usage

translate(seq, frame = 0, sens = "F", numcode = 1)

Arguments

seq

an object of class seq.

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 revers sense.

numcode

The number of the code to use. By default the standard genetic code is used.

Value

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

Details

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

{ 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 }

References

The genetic codes have been taken from the ncbi taxonomy database: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c. Last update October 05, 2000. The IUPAC one-letter code for aminoacids is described at: http://www.chem.qmul.ac.uk/iupac/AminoAcid/

To have an overview of the seqinR's functionnality, please consult this vignette: Charif, D., Lobry, J.R. (2005) SeqinR: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Springer Verlag, Biological and Medical Physics/Biomedical Series, in preparation.

Examples

Run this code

a=read.fasta(File=system.file("sequences/malM.fasta",package ="seqinr"))
translate(a[[1]])
translate(a[[1]],3,"R",6)

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