LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA

Table 2.

Performance of Aligners on theCFTR Region

Baboon Chimpanzee Mouse Rat Cow Pig Cat Dog Chicken Zebrafish Fugu Overall
Number of exons 232 176 230 230 224 174 176 182 68 48 150 1914
MUMmer
 100% 100 99 6 7 28 32 38 28 0 0 0 36
 90%–100% 100 100 8 9 40 44 47 37 0 0 0 41
 70%–100% 100 100 14 16 52 55 56 45 0 0 0 47
AVID
 100% 100 100 94 95 98 97 99 93 66 33 19 88
 90%–100% 100 100 98 100 99 100 100 98 79 42 21 91
 70%–100% 100 100 100 100 100 100 100 99 85 44 29 92
BlastZ
 100% 100 100 97 97 96 97 100 94 96 73 66 94
 90%–100% 100 100 100 100 98 100 100 99 97 79 72 97
 70%–100% 100 100 100 100 100 100 100 99 97 79 80 98
LAGAN
 100% 100 100 97 97 98 97 100 94 96 83 72 95
 90%–100% 100 100 100 100 99 100 100 99 99 88 77 98
 70%–100% 100 100 100 100 100 100 100 99 100 92 81 98
MLAGAN
 100% 100 100 97 97 98 97 100 94 99 88 73 96
 90%–100% 100 100 100 100 99 100 100 99 100 98 84 98
 70%–100% 100 100 100 100 100 100 100 99 100 100 90 99
Time (sec)
 MUMmer 8 6 7 7 8 6 6 6 3 2 2 61
 AVID 82 57 215 221 165 111 139 131 83 53 76 1775
 BlastZ 31 24 46 43 40 36 34 33 7 5 6 305
 LAGAN 56 50 78 82 60 68 62 78 338 158 133 1135
 MLAGAN — — — — — — — — — — — 4547
Max memory (MB)
 MUMmer 40 39 40 40 40 39 39 39 39 38 38 40
 AVID 598 551 581 584 578 498 522 502 387 340 360 598
 BlastZ 239 276 202 212 204 200 208 206 188 185 185 276
 LAGAN 90 90 90 89 90 87 88 87 88 87 89 90
 MLAGAN — — — — — — — — — — — 670

  • The annotated human exons were aligned with TBLASTN to createpseudo-annotations of exons in the other organisms. The table reports the percentage of exons covered by alignments over at least 70%, 90%, and 100% of their length, and the time and memory required to obtain the alignments. The last column reports the percentages of exons aligned out of total number of exons, the total time required for the 11 alignments (for the single 12-sequence multiple alignment in the case of MLAGAN), and the maximum memory required.

This Article

  1. Published in Advance March 12, 2003, doi: 10.1101/gr.926603 Genome Res. 13: 721-731

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