YOC, A new strategy for pairwise alignment of collinear genomes

Uricaru, Raluca; Michotey, Célia; Chiapello, Hélène; Rivals, Eric

doi:10.1186/s12859-015-0530-3

BMC Bioinformatics

Table 3 Quality of raw and filtered genome alignments produced by five genome aligners according to classical quality measures

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

*Lactobacillus* 14 intra-species alignments
	Mean number of segments before filtering	Mean alignment length [Cov] before filtering	Mean number of identities [%id] before filtering
NUCMER	108	2 010 305 [76.6]	1 985 563 [99.9]
MGA	33	2 267 771 [83]	2 155 141 [95.2]
MAUVE	2	2 895 734 [100]	2 389 905 [83.7]
PMAUVE	3	2 898 388 [99.7]	2 376 004 [83.1]
YOC	70	2 427 113 [90.8]	2 338 377 [96.2]
	Mean number of segments after filtering	Mean alignment length [Cov] after filtering	Mean number of identities [%id] after filtering
NUCMER	108	2 010 302 [76.6]	1 985 561 [99.9]
MGA	91	2 190 409 [81.6]	2 146 901 [98.0]
MAUVE	134	2 446 079 [91.7]	2 370 060 [96.8]
PMAUVE	111	2 419 589 [91]	2 365 075 [97.7]
YOC	109	2 368 669 [88.7]	2 328 734 [98.2]
*Bacillus cereus* 55 intra-species alignments
	Mean number of segments before filtering	Mean alignment length [Cov] before filtering	Mean number of identities [%id] before filtering
NUCMER	621	3 624 990 [69.4]	3 371 181 [92.3]
MGA	132	4 544 305 [83.5]	3 827 363 [83.4]
MAUVE	1	6 082 756 [100]	3 963 239 [65.5]
PMAUVE	33	6 043 087 [100]	3 869 392 [64.3]
YOC	313	4 448 646 [83.4]	3 907 562 [87.1]
	Mean number of segments after filtering	Mean alignment length [Cov] after filtering	Mean number of identities [%id] after filtering
NUCMER	621	3 624 978 [69.4]	3 371 172 [92.3]
MGA	418	4 186 007 [79.8]	3 790 894 [89.7]
MAUVE	564	4 418 643 [83.3]	3 884 906 [87.0]
PMAUVE	522	4 269 387 [81.2]	3 824 790 [88.7]
YOC	470	4 266 745 [81.5]	3 887 006 [90.3]

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. Values correspond to classical quality criteria (mean number of segments, mean alignment length, mean alignment coverage [Cov], mean number of identities and mean percentage of identities [%id]) before and after the GRAPe filtration procedure described in Section “Quality criteria”. Full results are given in Additional files 2 and 3.

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ISSN: 1471-2105

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