kmeRs_twoSeqSim {kmeRs}

kmeRs_twoSeqSim

Description

Supporting func to kmeRs_show_alignment

Usage

kmeRs_twoSeqSim(
  kmer_A,
  kmer_B,
  seq.type = "AA",
  submat = ifelse(test = (match.arg(toupper(seq.type), c("DNA", "AA")) == "AA"), yes =
    "BLOSUM62", no = NA),
  na.match = ifelse(is.na(submat), yes = 2, no = NA),
  na.mismatch = ifelse(is.na(submat), yes = -3, no = NA),
  align.type = "global",
  verbose = TRUE,
  ...
)

Arguments

kmer_A

given k-mer A

kmer_B

given k-mer B

seq.type

type of sequence in question, either 'DNA' or 'AA' (default)

submat

substitution matrix version, defaults to 'BLOSUM62'; other choices include 'BLOSUM45', 'BLOSUM50', 'BLOSUM62', 'BLOSUM80', 'BLOSUM100', 'PAM30', 'PAM40', 'PAM70', 'PAM120' and 'PAM250'; this parameter is ignored if na.match and na.mismatch are specified

na.match

for DNA sequences, what should the score for exact match be?

na.mismatch

for DNA sequences, what should the score for mismatches be?

align.type

"global" or "local"

verbose

= TRUE

...

other parameters, e.g. gap opening/extension penalties (gapOpening, gapExtension) for generating a DNA base substitution matrix