Figure 3. Running time of different SW implementations for real genomic read alignment.

Running time of aligning 1,000 real sequencing reads to various microorganism genomes and the human chromosome 1 are shown. Farrar’s implementation cannot handle long sequences as human chromosome 1, so its corresponding running time is not shown here. The log-scaled running time is shown on the y-axis for SSW without (blue) and with (red) detailed alignment, Farrar’s implementation (green), SSEARCH (pink) and an ordinary SW implementation (black). All SW implementations were tested under two sets of SW parameters: scores of match, mismatch, gap open and extension are 2, -1, -2, and -1 respectively (left), and scores of match, mismatch, gap open and extension are 1, -3, -5, and -2 respectively (right).