Editing Needleman–Wunsch algorithm (section)

===Gap penalty===
When aligning sequences there are often gaps (i.e. indels), sometimes large ones. Biologically, a large gap is more likely to occur as one large deletion as opposed to multiple single deletions. Hence two small indels should have a worse score than one large one. The simple and common way to do this is via a large gap-start score for a new indel and a smaller gap-extension score for every letter which extends the indel. For example, new-indel may cost -5 and extend-indel may cost -1. In this way an alignment such as:
 GAAAAAAT
 G--A-A-T
which has multiple equal alignments, some with multiple small alignments will now align as:
 GAAAAAAT
 GAA----T
or any alignment with a 4 long gap in preference over multiple small gaps.