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Figure 3 | Genome Biology

Figure 3

From: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Figure 3

The three phases of the Bowtie algorithm for the Maq-like policy. A three-phase approach finds alignments for two-mismatch cases 1 to 4 while minimizing backtracking. Phase 1 uses the mirror index and invokes the aligner to find alignments for cases 1 and 2. Phases 2 and 3 cooperate to find alignments for case 3: Phase 2 finds partial alignments with mismatches only in the hi-half, and phase 3 attempts to extend those partial alignments into full alignments. Finally, phase 3 invokes the aligner to find alignments for case 4.

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