Talk:Gap penalty

	This article is within the scope of WikiProject Molecular Biology, a collaborative effort to improve the coverage of Molecular Biology on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.Molecular BiologyWikipedia:WikiProject Molecular BiologyTemplate:WikiProject Molecular BiologyMolecular Biology articles
???	This article has not yet received a rating on the importance scale.
	This article is supported by the Computational Biology task force (assessed as High-importance).

External links modified

Hello fellow Wikipedians,

I have just added archive links to one external link on Gap penalty. Please take a moment to review my edit. If necessary, add {{cbignore}} after the link to keep me from modifying it. Alternatively, you can add {{nobots|deny=InternetArchiveBot}} 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

When you have finished reviewing my changes, please set the checked parameter below to true to let others know.

This message was posted before February 2018. After February 2018, "External links modified" talk page sections are no longer generated or monitored by InternetArchiveBot. No special action is required regarding these talk page notices, other than regular verification using the archive tool instructions below. Editors have permission to delete these "External links modified" talk page sections if they want to de-clutter talk pages, but see the RfC before doing mass systematic removals. This message is updated dynamically through the template {{source check}} (last update: 5 June 2024).

If you have discovered URLs which were erroneously considered dead by the bot, you can report them with this tool.
If you found an error with any archives or the URLs themselves, you can fix them with this tool.

Cheers.—^{cyberbot II}_{Talk to my owner:Online} 23:45, 8 January 2016 (UTC)[reply]

External links modified

Hello fellow Wikipedians,

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

When you have finished reviewing my changes, you may follow the instructions on the template below to fix any issues with the URLs.

This message was posted before February 2018. After February 2018, "External links modified" talk page sections are no longer generated or monitored by InternetArchiveBot. No special action is required regarding these talk page notices, other than regular verification using the archive tool instructions below. Editors have permission to delete these "External links modified" talk page sections if they want to de-clutter talk pages, but see the RfC before doing mass systematic removals. This message is updated dynamically through the template {{source check}} (last update: 5 June 2024).

If you have discovered URLs which were erroneously considered dead by the bot, you can report them with this tool.
If you found an error with any archives or the URLs themselves, you can fix them with this tool.

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

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)[reply]

Sounds good to me! Cheers, --Amkilpatrick (talk) 22:33, 3 March 2017 (UTC)[reply]

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)[reply]