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SSAHA
SSAHA (Sequence Search and Alignment by Hashing Algorithm) is a hashing-based method implemented to take advantage of large-RAM computers to increase search speed. The algorithm stores every k-mer in a sequence into a large hash table and searches for sequences based on matches with the hash table. SSAHA implements perfect hash and uses banded Smith-Waterman approach to extend the selected seeds.
http://europepmc.org/abstract/MED/11591649/reload=0;jsessionid=Wjl9VZXorUy6jL1oj1o3.2
http://www.sanger.ac.uk/resources/software/ssaha/
http://seqanswers.com/wiki/SSAHA
