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Table 1 Comparison of LAST and LASTM

From: A simple and economical method for improving whole genome alignment

Human vs mouse
 Alignment method Time (hours) No. of alignments Ave length Ave similarity
 LAST with D 3.04 2,521,923 842 61.29%
 LAST with 0.9D 6.19 2,616,550 837 61.03%
 LAST with 0.85D 11.85 2,665,216 834 60.95%
 Our method 3.72 2,642,403 838 60.99%
Human vs dog
 Alignment method Time (hours) No. of alignments Ave length Ave similarity
 LAST with D 3.18 4,533,937 905 62.99%
 LAST with 0.9D 6.65 4,640,443 898 62.85%
 LAST with 0.85D 12.30 4,640,877 895 62.78%
 Our method 3.87 4,657,968 899 62.84%
Human vs cat
 Alignment method Time (hours) No. of alignments Ave length Ave similarity
 LAST with D 4.36 4,431,635 908 62.62%
 LAST with 0.9D 7.84 4,526,245 901 62.51%
 LAST with 0.85D 13.26 4,571,706 899 62.46%
 Our method 5.29 4,541,363 902 62.51%
Human vs cow
 Alignment method Time (hours) No. of alignments Ave length Ave similarity
 LAST with D 4.59 6,437,907 785 61.65%
 LAST with 0.9D 7.83 6,724,264 775 61.47%
 LAST with 0.85D 12.78 6,875,343 770 61.38%
 Our method 5.34 6,770,810 778 61.44%
Human vs rat
 Alignment method Time (hours) No. of alignments Ave length Ave similarity
 LAST with D 4.16 8,055,476 505 62.29%
 LAST with 0.9D 7.78 8,563,474 504 62.07%
 LAST with 0.85D 13.27 8,836,291 503 61.96%
 Our method 4.86 8,595,871 509 62.07%
  1. Both LAST and LASTM use the HOXD70 [4] scoring scheme, and their gap existence and extension penalties are -400 and -30 respectively. Their minimum score of gapped alignments is 4500. For LAST, its default minimum score of gapless alignments is D=962, and for LASTM, it is 674 (≈0.7D). The distance d for the filtering step of LASTM is 2000