translate {seqinr}R Documentation

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.

Details

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

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 '*'.

Author(s)

D. Charif

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.

See Also

SEQINR.UTIL

Examples

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

[Package seqinr version 1.0-2 Index]