translate {seqinr} | R Documentation |
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.
translate(seq, frame = 0, sens = "F", numcode = 1)
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. |
The following genetic codes are described here. The number preceding each code corresponds to numcode
.
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 '*'.
D. Charif
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.
a=read.fasta(File=system.file("sequences/malM.fasta",package ="seqinr")) translate(a[[1]]) translate(a[[1]],3,"R",6)