Abstract
Dynamic programming [1] has full sensitivity, but too slow for large scale homology search. FASTA/BLAST type of heuristics [2] trade sensitivity for speed. Can we have both sensitivity and speed?
We present the mathematical theory of optimized spaced seeds which allows modern homology search to achieve high sensitivity and high speed simultaneously. The spaced seed methodology is implemented in our Pattern Hunter software [3, 4], as well as many other modern homology search software, serving thousands of queries daily.
The theory is then extended and implemented in ZOOM [5] to do fast genome scale reads mapping for the second generation sequencers.
