needleman {ftrCOOL}

Needleman-Wunsch (needleman)

Description

This function works based on Needleman-Wunsch algorithm which computes similarity score of two sequences.

Usage

needleman(seq1, seq2, gap = -1, mismatch = -1, match = 1)

Arguments

seq1

(sequence1) is a string.

seq2

(sequence2) is a string.

gap

The penalty for gaps in sequence alignment. Usually, it is a negative value.

mismatch

The penalty for the mismatch in the sequence alignment. Usually, it is a negative value.

match

A score for the match in sequence alignment. Usually, it is a positive value.

Value

The function returns a number which indicates the similarity between sequence1 and sequence2.

References

https://gist.github.com/juliuskittler/ed53696ac1e590b413aac2dddf0457f6

Examples

simScore<-needleman(seq1="Hello",seq2="Hello",gap=-1,mismatch=-2,match=1)