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.)
Comments
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