globalAlignnmentNeedlemanWunsch: Needleman Wunsch

In BeatriceBa/RProjectNW: Perform Needleman-Wunsch algorithm

Description

Core function of the package, performs the Needleman-Wunsch algorithm

Usage

globalAlignnmentNeedlemanWunsch(
  matchCost,
  mismatchCost,
  gapPenalty,
  sequenceA,
  sequenceB
)

Arguments

matchCost	The cost of a match
mismatchCost	The cost of a mismatch
gapPenalty	The gap penalty(cost of gap/indel)
sequenceA	The first nucleotide sequence (positioned on the rows)
sequenceB	The second nucleotide sequence (positioned on the columns)

Value

a list containing the score matrix, the direction matrix, the first alignment, the second alignment

References

https://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm

Examples

sequenceA <- "GTT"
sequenceB <- "GCATT"
matchCost <- 7
mismatchCost <- -3
gapPenalty <- -4
result <- globalAlignnmentNeedlemanWunsch(matchCost,mismatchCost,gapPenalty,sequenceA,sequenceB)

BeatriceBa/RProjectNW documentation built on Dec. 17, 2021, 10:47 a.m.