trans {ape} | R Documentation |
trans
translates DNA sequences into amino acids.
complement
returns the (reverse) complement sequences.
trans(x, code = 1, codonstart = 1) complement(x)
x |
an object of class |
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. |
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
.
an object of class "AAbin"
or "DNAbin"
, respectively.
These functions are equivalent to translate
and comp
in
the package seqinr with the difference that there is no need to
convert the sequences into character strings.
Emmanuel Paradis
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes
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