ape (version 4.0)

trans: Translation from DNA to Amino Acid Sequences

Description

trans translates DNA sequences into amino acids. complement returns the (reverse) complement sequences.

Usage

trans(x, code = 1, codonstart = 1)
complement(x)

Arguments

x

an object of class "DNAbin" (vector, matrix or list).

code

an integer value giving the genetic code to be used. Currently only 1 (standard code) and 2 (vertebrate mitochondrial code) are supported.

codonstart

an integer giving where to start the translation. This should be 1, 2, or 3, but larger values are accepted and have for effect to start the translation further within the sequence.

Value

an object of class "AAbin" or "DNAbin", respectively.

Details

With trans, if the sequence length is not a multiple of three, a warning message is printed. Alignment gaps are simply ignored (i.e., AG- returns X with no special warning or message). Base ambiguities are taken into account where relevant: for instance, GGN, GGA, GGR, etc, all return G.

References

http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes

See Also

AAbin, checkAlignment, alview

Examples

data(woodmouse)
X <- trans(woodmouse) # not correct
X2 <- trans(woodmouse, 2) # using the correct code
identical(X, X2)
alview(X[1:2, 1:60]) # some codon Stop (*)
alview(X2[, 1:60])
X2