ape (version 5.8)

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)

Value

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

Arguments

x

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

code

an integer value giving the genetic code to be used. Currently only the genetic codes 1 to 6 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 towards the 3'-end of the sequence.

Author

Emmanuel Paradis

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.

See the link given in the References for details about the taxonomic coverage and alternative codons of each code.

References

https://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 'Stop' codons (*)
alview(X2[, 1:60])
X2