| Hmm, while I understand the problem of gapping is traditionally the hard part, I'm under the impression that the argument you're putting forward is primarily one of semantics. "In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences." (From the article you linked.) Gapped sequence alignment is certainly far more robust (and biologically relevant - insertions are a common error - when comparing sequences across organisms) than ungapped, and a much harder problem, but as for the definition of "alignment" itself, I don't believe I've misnamed anything here. If we're going to be overly pedantic about the use of the word "alignment" that's fine, but I'm not sure it's a worthwhile debate to have. A quick search for "ungapped sequenced alignment" returns a great deal of results on Google [1]. So if I am mistaken, I'm certainly not the first (nor do I believe I'll be the last.) Furthermore, there's nothing preventing anybody from using the methods described here from implementing an ungapped sequence alignment tool that outperforms tools that only use string comparisons. :) [1] https://www.google.com/search?q=ungapped%20sequence%20alignm.... |
tools like BLAST are extremely sophisticated and have been under development for decades, and I'm fairly confident they've moved past naive string comparisons by now.