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GapPenalty

is an option for SequenceAlignment and related functions that gives the additional cost associated with each gap corresponding to a run of insertions or deletions.

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GapPenalty

GapPenalty

is an option for SequenceAlignment and related functions that gives the additional cost associated with each gap corresponding to a run of insertions or deletions.

Details

  • GapPenalty->p specifies that the similarity of sequences should have an amount p subtracted for every run of insertions or deletions needed to align the sequences.

Examples

Basic Examples  (2)

By default, an alignment is found with two gaps:

Wolfram Language code: SequenceAlignment["ac", "abcd"]

Increasing the penalty for gaps forces another alignment with fewer gaps:

Wolfram Language code: SequenceAlignment["ac", "abcd", GapPenalty -> 2]

The default alignment score:

Wolfram Language code: NeedlemanWunschSimilarity["aaaaaacccccc", "aaaaaabbbcccccc"]

Add an additional penalty for the gap:

Wolfram Language code: NeedlemanWunschSimilarity["aaaaaacccccc", "aaaaaabbbcccccc", GapPenalty -> 1]
Wolfram Research (2008), GapPenalty, Wolfram Language function, https://reference.wolfram.com/language/ref/GapPenalty.html.

Text

Wolfram Research (2008), GapPenalty, Wolfram Language function, https://reference.wolfram.com/language/ref/GapPenalty.html.

CMS

Wolfram Language. 2008. "GapPenalty." Wolfram Language & System Documentation Center. Wolfram Research. https://reference.wolfram.com/language/ref/GapPenalty.html.

APA

Wolfram Language. (2008). GapPenalty. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/GapPenalty.html

BibTeX

@misc{reference.wolfram_2026_gappenalty, author="Wolfram Research", title="{GapPenalty}", year="2008", howpublished="\url{https://reference.wolfram.com/language/ref/GapPenalty.html}", note=[Accessed: 13-June-2026]}

BibLaTeX

@online{reference.wolfram_2026_gappenalty, organization={Wolfram Research}, title={GapPenalty}, year={2008}, url={https://reference.wolfram.com/language/ref/GapPenalty.html}, note=[Accessed: 13-June-2026]}