Determining promoter location based on DNA structure first-principles calculations

Table 2 Global ASM performance index obtained by considering Bajic's muti-metric analysis for different sets of genes

	CDS_gene	no_CDS_gene	noCpG	no_CpG_CAGE
ProStar	2.78	2.00	6.56	2.56
cpgprod	8.22	7.89	7.22	7.11
dgsf	9.56	9.11	9.11	7.00
dpf	6.78	7.00	4.89	5.67
eponine	5.56	6.11	8.33	3.78
firstef	4.00	4.00	5.56	3.78
fprom	3.56	3.22	2.78	9.78
mcpromoter	5.56	5.33	4.89	4.89
nnpp	10.44	10.33	9.44	8.89
nscan	1.56	2.89	1.22	6.89
promoter2.0	10.67	10.56	8.89	9.33
proscan	9.33	9.56	9.11	8.33

Global ASM performance index obtained following Bajic's muti-metric analysis (see Materials and methods) for different sets of genes: the 2,641 TSSs from the Havana set (column CDS_gene), the 1,764 TSSs of non-coding genes from the Havana set (column no_CDS_gene), the 1,751 TSSs of the Havana set that do not overlap any CpG island (column noCpG), and the collection of 1,086 Cage TSSs not associated with CpG islands (no_CpG_CAGE). In each case the method providing the best results is shown in bold. Note that ProStar is the best in the two most difficult categories and the second best over the entire set of genes.

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