Note: These tutorials are incomplete. More complete versions are being made available for our members. Sign up for free.

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


Web Statistics