Skip to main content

Table 4 Quality of genome alignments produced by five genome aligners according to our new qualitative criterion

From: YOC, A new strategy for pairwise alignment of collinear genomes

 

GRA-FIL average (in number of pos. and [%])

GRA-FIL minimum (in number of pos.)

GRA-FIL maximum (in number of pos.)

Lactobacillus 14 intra-species alignments

NUCMER

2 [0.00%]

0

5

MGA

77 362 [1.47%]

59

157 619

MAUVE

449 655 [8.31%]

0

802 632

PMAUVE

478 799 [8.66%]

0

866 011

YOC

58 445 [1.27%]

0

125 821

Bacillus cereus 55 intra-species alignments

NUCMER

10 [0.00%]

0

158

MGA

358 298 [7.63%]

143 412

436 054

MAUVE

1 664 114 [22.45%]

592 079

2 950 027

PMAUVE

1 773 700 [24.70%]

666 595

3 390 532

YOC

181 900 [4.5%]

71 851

262 813

  1. Part 1 of the table corresponds to the 14 intra-species pairwise genome alignments of the Lactobacillus genus. Part 2 of the table corresponds to the 55 intra-species pairwise genome alignments of the Bacillus cereus species. The software compared are: MUMmer (NUCmer), MGA, MAUVE, ProgressiveMAUVE (PMAUVE) and YOC. The values in the table correspond to the average, the maximum and the minimum results using the GRA-FIL criterion, i.e. the number and the percentage of the likely erroneous alignment positions that were filtered by the GRAPe filtration procedure described in Section “Quality criteria”. Full results are given in Additional files 2 and 3.