cdsstring2codonaln: cdsstring2codonaln

In kullrich/MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

cdsstring2codonaln

Description

This function takes two sequences as DNAStringSet, and their corresponding AAStringSet, calculates a global alignment and converts this alignment back into a codon alignment.

Usage

cdsstring2codonaln(
  cds,
  aa,
  type = "global",
  substitutionMatrix = "BLOSUM62",
  gapOpening = 10,
  gapExtension = 0.5,
  remove.gaps = FALSE
)

Arguments

cds	two sequences DNAStringSet [mandatory]
aa	two sequences AAStringSet [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]

Value

codon alignment as DNAStringSet

Author(s)

Kristian K Ullrich

References

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

See Also

pairwiseAlignment

Examples

## define two cds sequences
cds <- Biostrings::DNAStringSet(c("ATGCAACATTGC", "ATGCATTGC"))
names(cds) <- c("cds1", "cds2")
## get protein alignment
aa <- MSA2dist::cds2aa(cds)
cdsstring2codonaln(cds, aa)

kullrich/MSA2dist documentation built on Nov. 14, 2024, 5:39 p.m.