How I Wrote an Ultra-Fast DNA Sequence Alignment Algorithm in JavaScript

Re:How I Wrote an Ultra-Fast DNA Sequence Alignment Algorith... by lightlike on Monday February 23, 2015 @05:05PM (#9097356)

you shouldn't dismiss this as an argument over semantics if your understanding of the term differs from researchers' use of the term. if you introduce "a fast tool for XYZ" and researchers understand XYZ to mean A, where you understand it to mean B, then the tool is not useful for researchers to perform what they know as XYZ.

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.

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Re:How I Wrote an Ultra-Fast DNA Sequence Alignment Algorith... by keithwhor on Monday February 23, 2015 @06:08PM (#9097655)

Fair. Though I'm not convinced "ungapped sequence alignment" is particularly confusing to a researcher, considering there are tools and papers that have existed for decades using this description [1][2][3]. Though the algorithm described in my article is extremely focused on raw performance (and relatively naive with scoring), I would still choose to categorize it as primarily a tool that deals with ungapped sequence alignment, specifically supporting IUPAC degenerate nucleotide sequences. Thus, I believe the initial argument is, indeed, overly pedantic.

And to be clear, nowhere am I comparing what I've developed to BLAST. (They have very different applications.)

[1] http://schneider.ncifcrf.gov/paper/malign/

[2] http://www.ncbi.nlm.nih.gov/pubmed/9697204

[3] http://www.ncbi.nlm.nih.gov/pubmed/15130540

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