obAnalytics (version 0.1.1)

alignS: Align 2 sequences.

Description

Verbatim implementation of Needleman-Wunsch matching algorithm.

Usage

alignS(s.matrix, gap = -1)

Arguments

s.matrix

Similarity matrix. See sMatrix(...).

gap

Penality assigned to a gap (missing or extra value).

Value

2 column matrix. First column = similarity matrix rows (first sequence), Second column = similarity matrix columns (second sequence). Each row maps aligned indexs from each sequence:

  > a <- c(2,4,5)
  > b <- 1:5
  > alignS(sMatrix(a,b))
       a b
  [1,] 1 2
  [2,] 2 4
  [3,] 3 5

References

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

Examples

## Not run: 
# 
# a <- c(2,4,5)
# b <- 1:5
# alignS(sMatrix(a, b))
# 
# ## End(Not run)