Table 12.

Alignment Times in Seconds of 10,000 ESTs (Average Size 380 Bases) Against Human Genomic Sequence Using Various K Sizes and N Sizes

K	N	2×106	2×107	2×108
10	2	3.9	35.6	680.1
10	3	3.2	21.4	348.7
11	2	2.4	8.1	92.4
11	3	2.3	6.5	61.8
12	2	3.9	7.0	39.9
12	3	3.7	6.4	33.8

The 2 × 10⁶ genomic sequence is ctg12414, which is 2,034,363 bases long and was taken from the December 2000 UCSC human genome assembly (http://genome.ucsc.edu). The 2 × 10⁷ genomic sequence is ctg15424 and is 20,341,418 bases long. The 2 × 10⁸ column is chromosome 4 and is 200,175,155 bases long. The two major components of the run-time are the time it takes to bin and sort the K-mer hits (clumping is almost instantaneous after sorting), and the time it takes to extend the clumps into alignments. The bin/sort time depends on the number of hits, which is proportional to 4^−K. The bin/sort time is somewhere between O(n) and O(n log n). The extend time is linear with respect to the number of clumps.