DNAtoAA | R Documentation |
Convert DNA sequences to amino acid peptides, in 1 or more reading frames
DNAtoAA(dna, clipAtStop = TRUE, readingFrames=1:6)
DNAVtoAAV(dnaVec)
DNAtoBestPeptide( dnaSet, clipAtStop = FALSE, readingFrames=1:6)
DNAtoFrameShiftingPeptides( dnaSet, min.aa.length=10)
dna |
character string of length 1, containing a sequence of nucleic acid one letter codes |
dnaSet |
character vector of DNA sequences |
strand |
coding strand that |
clipAtStop |
should conversion stop after encountering the first stop codon |
readingFrames |
a vector of reading frame numbers, from 1-6, where 4-6 are the 3 reading frames on the reverse strand |
dnaVec |
character vector of single letter nucleic acids |
min.aa.length |
the shortest peptide fragment wanted returned after conversion |
Facilitates converting DNA sequences to amino acid sequences. The first form is moderately fast, and you choose which reading frames to use. The third form is fastest, expecting a vector of single nucleotides in frame.
All use the codon definitions table from the getCodonMap
Function DNAtoBestPeptide
is a wrapper function that takes 1 or more DNA sequences,
translates them in all 6 reading frames and selects the best amino acid sequence for each.
Best is defined as the reading frame yielding the longest peptide with no stop codons.
Function DNAtoFrameShiftingPeptides
is a wrapper function that takes 1 or more DNA sequences,
assumed to be from the coding strand, and finds all suitably long protein fragments, assuming that
there may be reading frame shift errors due to sequencing base caller, etc.
For DNAtoAA()
, a character vector of length 1 to 6, giving the amino acid sequences. The names are the read frame numbers.
For DNAVtoAAV()
, a character vector of single amino acids, of length
length(dnaVec)/3
.
The stop codon is explicitly included. Invalid DNA triplets, as from 'N's, cause '?'s in the amino acid sequence.
For DNAtoBestPeptide()
, a character vector of the same length as dnaSet
, with the one best
peptide sequence for each DNA sequence.
For DNAtoFrameShiftingPeptides()
, a data frame, or a list of data frames of the same
length as dnaSet
, with all the sufficiently long peptide sequences and their locations, for each DNA sequence.
getCodonMap
, to get the conversion table of DNA triples to amino acids.
AAtoCodonOptimizedDNA
, to convert from DNA to protein amino acids.
DNAtoAA( "ATGAAACGGTAGANACCCGGG", clipAtStop=TRUE, readingFrames=1:6)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.