Figure 1.

Hash tables for three methods. Three methods to find genome positions of 1-mismatch from the subsequence AAGT. Genome position 1000 is ACGT, which is the 1-mismatch of the subsequence. The first method refers to the hash table 16 times. The second method refers to the table just once, but the table is 16-fold larger. The third method refers to the table three times. After getting position 1002 from the hash table, the method elongates the alignment toward the front of the sequence.

Takenaka et al. BMC Genomics 2011 12(Suppl 3):S8   doi:10.1186/1471-2164-12-S3-S8