There is a string search based on the BWT which is used for most DNA read mapping these days due to its favorable performance compared to existing hash based algorithms.
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.
General alignment definitely is quite different, however The vast majority of sequence data that's produced these days are short reads. Read-mapping is a much lower-bar and more similar to string search than proper sequence alignment. The BWT-based search [1] is a bit more practical with the small alphabet size of DNA compared to most human texts, however.
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There is a string search based on the BWT which is used for most DNA read mapping these days due to its favorable performance compared to existing hash based algorithms.
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
Sequence alignment and string search are different enough problems that we really should distinguish between them.
General alignment definitely is quite different, however The vast majority of sequence data that's produced these days are short reads. Read-mapping is a much lower-bar and more similar to string search than proper sequence alignment. The BWT-based search [1] is a bit more practical with the small alphabet size of DNA compared to most human texts, however.
http://people.unipmn.it/manzini/papers/focs00draft.pdf
So can any of here other string search algos be used for DNA mapping?