Talk:Gap penalty

External links modified
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I have just added archive links to 1 one external link on Gap penalty. Please take a moment to review my edit. If necessary, add after the link to keep me from modifying it. Alternatively, you can add to keep me off the page altogether. I made the following changes:
 * Added archive https://web.archive.org/20120620133216/http://www.ebi.ac.uk:80/help/gaps.html to http://www.ebi.ac.uk/help/gaps.html

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External links modified
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I have just modified one external link on Gap penalty. Please take a moment to review my edit. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit this simple FaQ for additional information. I made the following changes:
 * Added archive https://web.archive.org/web/20130626060959/http://www.biogem.org:80/downloads/notes/Gap%20Penalty.pdf to http://www.biogem.org/downloads/notes/Gap%20Penalty.pdf

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Cheers.— InternetArchiveBot  (Report bug) 21:51, 7 January 2017 (UTC)

Wikitext instead of JPGs
Would it be OK to replace the JPGs by wikitext?

ATTGAC

||  |

AT---C

--Nothingserious (talk) 16:10, 3 March 2017 (UTC)
 * Sounds good to me! Cheers, --Amkilpatrick (talk) 22:33, 3 March 2017 (UTC)

Does it really make sense to include `diff`, spellcheckers, or plagiarism checkers in the list of "applications"?
All of these are examples where simply calculating a Levenshtein distance or LCS distance works fine - i.e. where you'd normally use a concept of edit distance that assigns a fixed cost to each single character insertion or deletion (or substitution or transposition, maybe). The `diff` util, for instance, uses the Myers diff algorithm, and Myers's paper (http://www.xmailserver.org/diff2.pdf) literally does not use the word "gap" anywhere nor refer to the concept by any other name.

I guess you can pedantically argue that all edit distance metrics that assign a per-character cost to insertions and deletions ARE using a gap penalty - namely a linear gap penalty. But it seems very weird to me to describe this as an application of the concept given that you don't need to the concept of a "gap penalty" to define those edit distances or write algorithms using them.

Perhaps a useful analogy: it seems a bit like describing addition of integers as an "application" of arithmetic on the complex numbers. Like, okay, if you really want to then you can frame LCS distance as the special case of sequence-alignment-with-gap-penalty where the gap penalty is specified to be linear, just as you can frame addition of real numbers as a special case of addition of complex numbers where the imaginary part is specified to be zero, but it's still not an application of the broader and more abstract concept!

I am in favour of ripping out all three of those "applications" and instead having a sentence noting that diffing algorithms or edit distance metrics like Myers diff or Levenshtein distance, though normally defined by describing the cost of a single-character insertion or deletion, can instead be equivalently regarded as using a linear gap penalty.

~ ExplodingCabbage (talk) 17:22, 22 December 2023 (UTC)