| backTranslate {microseq} | R Documentation |
Replace amino acids with codons
Description
Replaces aligned amino acids with their original codon triplets.
Usage
backTranslate(aa.msa, nuc.ffn)
Arguments
aa.msa |
A fasta object with a multiple alignment, see |
nuc.ffn |
A fasta object with the coding sequences, see |
Details
This function replaces the aligned amino acids in aa.msa with their
original codon triplets. This is possible only when the nucleotide sequences in nuc.ffn
are the exact nucleotide sequences behind the protein sequences that are aligned in aa.msa.
It is required that the first token of the ‘Header’ lines is identical for a protein sequence
in aa.msa and its nucleotide version in ‘nuc.ffn’, otherwise it is impossible to
match them. Thus, they may not appear in the same order in the two input fasta objects.
When aligning coding sequences, one should in general always align their protein sequences, to
keep the codon structure, and then use backTranslate to convert this into a
nucleotide alignment, if required.
If the nuclotide sequences contain the stop codons, these will be removed.
Value
A fasta object similar to aa.msa, but where each amino acid has been replace by
its corresponding codon. All gaps ‘"-"’ are replaced by triplets ‘"---"’.
Author(s)
Lars Snipen.
See Also
Examples
msa.file <- file.path(file.path(path.package("microseq"),"extdata"), "small.msa")
aa.msa <- readFasta(msa.file)
nuc.file <- file.path(file.path(path.package("microseq"),"extdata"), "small.ffn")
nuc <- readFasta(nuc.file)
nuc.msa <- backTranslate(aa.msa, nuc)