SSAHA is a software tool for very fast matching and alignment of DNA
sequences. It stands for Sequence Search and Alignment by Hashing
Algorithm. It achieves its fast search speed by converting sequence
information into a `hash table' data structure, which can then be
searched very rapidly for matches.

SSAHA: a fast search method for large DNA databases (2001).
Ning Z, Cox AJ, Mullikin JC. Genome Res. 11: 1725-9. 
PMID: 11591649

WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/