Editing Needleman–Wunsch algorithm (section)

===Basic scoring schemes===
The simplest scoring schemes simply give a value for each match, mismatch and indel. The step-by-step guide above uses match = 1, mismatch  = −1, indel = −1. Thus the lower the alignment score the larger the [[Levenshtein distance|edit distance]], for this scoring system one wants a high score. Another scoring system might be:
* Match = 0
* Indel = -1
* Mismatch = -1

For this system the alignment score will represent the edit distance between the two strings.
Different scoring systems can be devised for different situations, for example if gaps are considered very bad for your alignment you may use a scoring system that penalises gaps heavily, such as:

* Match = 1
* Indel = -10
* Mismatch = -1