Figure 6.

Kernel pseudo code. Each thread executes this code on a different database sequence. The pseudo-code for the Smith-Waterman implementation is made up of the outer loop, which cycles on the database sequence characters, followed by the inner loop, which does the basic dynamic programming calculations.

Manavski and Valle BMC Bioinformatics 2008 9(Suppl 2):S10   doi:10.1186/1471-2105-9-S2-S10