cds2codonaln

This function takes two single sequence DNAString's or two single sequence DNAStringSet's, converts them into aa, calculates a global alignment and converts this alignment back into a codon alignment.

cds2codonaln(
  cds1,
  cds2,
  type = "global",
  substitutionMatrix = "BLOSUM62",
  gapOpening = 10,
  gapExtension = 0.5,
  remove.gaps = FALSE,
  ...
)

Arguments

cds1

single sequence DNAStringSet or DNAString [mandatory]

cds2

single sequence DNAStringSet or DNAString [mandatory]

type

type of alignment (see pairwiseAlignment) [default: global]

substitutionMatrix

substitution matrix representing the fixed substitution scores for an alignment (see pairwiseAlignment) [default: BLOSUM62]

gapOpening

the cost for opening a gap in the alignment (see pairwiseAlignment) [default: 10]

gapExtension

the incremental cost incurred along the length of the gap in the alignment (see pairwiseAlignment) [default: 0.5]

remove.gaps

specify if gaps in the codon alignment should be removed [default: FALSE]

...

other cds2aa parameters

Value

codon alignment as DNAStringSet

References

Pagès, H et al. (2014) Biostrings: Efficient manipulation of biological strings. R package version, 2(0).

See also

pairwiseAlignment

Author

Kristian K Ullrich

Examples

## define two cds sequences
cds1 <- Biostrings::DNAString("ATGCAACATTGC")
cds2 <- Biostrings::DNAString("ATGCATTGC")
cds2codonaln(cds1, cds2)
#> DNAStringSet object of length 2:
#>     width seq                                               names               
#> [1]    12 ATGCAACATTGC                                      cds1
#> [2]    12 ATG---CATTGC                                      cds2