Comment on Faster string searching and matching with Rabin-Karp algorithmparentComments−ahelwer14yYou are probably thinking of Smith-Waterman:http://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorith...Company I work at (in HPC) was in negotiations to implement it for one of those big plant biotech firms long before I was around, or so I have been told.−epistasis14ySmith-Waterman is the gold standard, but it's too slow for most applications so many heuristics have been developed.BWA is the most popular tool these days for short-read mapping, and has a Smith-Waterman based approach for long reads as well:http://bio-bwa.sourceforge.net/bwa.shtml
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You are probably thinking of Smith-Waterman:
http://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorith...
Company I work at (in HPC) was in negotiations to implement it for one of those big plant biotech firms long before I was around, or so I have been told.
Smith-Waterman is the gold standard, but it's too slow for most applications so many heuristics have been developed.
BWA is the most popular tool these days for short-read mapping, and has a Smith-Waterman based approach for long reads as well:
http://bio-bwa.sourceforge.net/bwa.shtml