trans: Translation from DNA to Amino Acid Sequences

In ape: Analyses of Phylogenetics and Evolution

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 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.

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.

Value

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

Note

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.

Author(s)

Emmanuel Paradis

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

ape documentation built on May 29, 2024, 10:50 a.m.