Editing Needleman–Wunsch algorithm (section)

===Choosing a scoring system===
Next, decide how to score each individual pair of letters. Using the example above, one possible alignment candidate might be:
 12345678
 {{DNA sequence|GCATG-CG}}
 {{DNA sequence|G-ATTACA}}

The letters may match, mismatch, or be matched to a gap (a deletion or insertion ([[indel]])):
* Match: The two letters at the current index are the same.
* Mismatch: The two letters at the current index are different.  
* Indel (Insertion or Deletion): The best alignment involves one letter aligning to a gap in the other string.

Each of these scenarios is assigned a score and the sum of the scores of all the pairings is the score of the whole alignment candidate. Different systems exist for assigning scores; some have been outlined in the [[#Scoring systems|Scoring systems]] section below. For now, the system used by Needleman and Wunsch<ref name="Needleman"/>{{verification failed|reason=Needleman and Wunsch use 1 and 0 not 1 and -1|date=October 2024}} will be used:

* Match: +1
* Mismatch or Indel: −1

For the Example above, the score of the alignment would be 0:
 {{DNA sequence|GCATG-CG}}
 {{DNA sequence|G-ATTACA}}
 +−++−−+− −> 1*4 + (−1)*4 = 0