It seems to me as though the authors are unfamiliar with bioinformatics standard practice - it's not like this is an unsolved problem, and the existing solutions are faster, more computationally elegant, and more flexible. Actually computing and searching for all strings with an edit distance of X away from the query is an incredibly poor way (Guess how long their strategy takes when you increase the edit distance to 5?) of of solving the alignment problem that throws out 40+ years of research on the problem of sequence alignment. The actual solutions to this problem solve it in tenths of a second in vastly superior ways.
BLAT[0] is the most obvious and preferred solution designed for alignment against a reference sequence- a 20 BP search against the human genome should essentially be instantaneous. BLAST [1] is more versatile and a bit slower than BLAT, but would also align these sequence sizes against the human genome in ~1-2 seconds, and is a traditional solution to the alignment problem, and has no license restrictions. BWA [2] and Bowtie [3] default settings could also be modified for the task (they're optimized for performing this task with larger strings on the order of thousands of times per second).
More generally, it would not be difficult to re-implement any of the algorithms behind these software implementations if the authors really wanted to. It's weird, this is the second post I've seen recently when software folks who are now working in the bioinformatics space have seemed completely unaware of both the basic algorithms we use in computational biology and their common implementations, like Smith-Waterman and Burrows–Wheeler. These are complicated problems with 40+ years of research behind them, and the actual solutions are elegant and fast algorithms which solve the problem in a far superior way within reasonable computational time.
[0] http://genome.ucsc.edu/cgi-bin/hgBlat
[1] http://blast.ncbi.nlm.nih.gov/
[2] http://bio-bwa.sourceforge.net/
[3] http://bowtie-bio.sourceforge.net/index.shtml
BLAT[0] is the most obvious and preferred solution designed for alignment against a reference sequence- a 20 BP search against the human genome should essentially be instantaneous. BLAST [1] is more versatile and a bit slower than BLAT, but would also align these sequence sizes against the human genome in ~1-2 seconds, and is a traditional solution to the alignment problem, and has no license restrictions. BWA [2] and Bowtie [3] default settings could also be modified for the task (they're optimized for performing this task with larger strings on the order of thousands of times per second).
More generally, it would not be difficult to re-implement any of the algorithms behind these software implementations if the authors really wanted to. It's weird, this is the second post I've seen recently when software folks who are now working in the bioinformatics space have seemed completely unaware of both the basic algorithms we use in computational biology and their common implementations, like Smith-Waterman and Burrows–Wheeler. These are complicated problems with 40+ years of research behind them, and the actual solutions are elegant and fast algorithms which solve the problem in a far superior way within reasonable computational time.
[0] http://genome.ucsc.edu/cgi-bin/hgBlat
[1] http://blast.ncbi.nlm.nih.gov/
[2] http://bio-bwa.sourceforge.net/
[3] http://bowtie-bio.sourceforge.net/index.shtml