Research Article

Designing Efficient Spaced Seeds for SOLiD Read Mapping

Table 4

Comparison of 4 different seed families on the S. cerevisiae dataset.

Seed family Mapped reads Unique mapping positions Execution time

PerM-F3-S20 768,732 (60.03%) 694,951 (54.27%) 0m55s
SHRiMP-default 836,899 (65.36%) 751,761 (58.71%) 2m15s
3-lossy-12 839,633 (65.57%) 754,402 (58.91%) 2m10s
3-lossless-10-24p 839,072 (65.53%) 755,208 (58.98%) 2m06s