Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction

BMC Bioinformatics

Table 1 Comparison of the gene order reconstruction of the primate-rodent ancestral X-chromosome using MGRA2, FPMAG and MULTIRES

	Conserved	MGRA2	FPMAG	MultiRes
Genes	746	132	429	518.12 (19.81)
Adjacencies	749	130	350	468.31 (6.05)
Recovered	-	42	350	468.31 (6.05)
Fragments	N/A	1	79	53.16 (4.76)

The row for total adjacencies indicates the number of adjacencies found in the reconstruction. The third row indicates the number of reconstructed adjacencies which are conserved in 2 or more descendant species. Note that FPMAG and MultiRes only recover conserved adjacencies. MGRA2 can also limit the number of CARs reconstructed and find a single CAR. The results for MultiRes are averaged over all parameter combinations. The low standard deviations demonstrate the robustness of the method to parameter choices

ISSN: 1471-2105