translate {microseq} | R Documentation |
The translation from DNA(RNA) to amino acid sequence according to the standard genetic code.
translate(nuc.sequences, M.start = TRUE, no.stop = TRUE, trans.tab = 1)
nuc.sequences |
Character vector containing the nucleotide sequences. |
M.start |
A logical indicating if the amino acid sequence should start with M regardless of start codon (ATG, GTG or TTG). |
no.stop |
A logical indicating if terminal stops (*) should be eliminated from the translated sequence |
trans.tab |
Translation table, either 1 or 4 |
Translating DNA or RNA to protein. Possible start codons are ATG, GTG or TTG. Stop codons are TAA, TGA, TAG. All codons are
translated accoring to the Stadard geneti code. This is translation table 1. The only alternative implemented here is translation
table 4, which is used by some bacteria (e.g. Mycoplasma, Mesoplasma). If trans.tab
is 4, the stop codon TGA is
translated to W (Tryptophan).
A character vector of translated sequences.
Lars Snipen and Kristian Hovde Liland.
ex.file <- file.path(file.path(path.package("microseq"),"extdata"),"small.fasta") fdta <- readFasta(ex.file) translate(fdta$Sequence)