Tools for the identification of variable and potentially variable tandem repeats

BMC Genomics

Table 2 Comparisons between VNTRfinder and the method described by Denoeud and Vergnaud.

Mycobacterium tuberculosis(99.3% identical)					Neisseria meningitidis(48.74% identical)
	Total	% Denoeud aligned TRs aligned by VNTRfinder	% of Denoeud VNTRs called by VNTRfinder as variant or non-variant	% of Denoeud non-variants called by VNTRfinder as variant or non-variant		Total	% Denoeud aligned TRs aligned by VNTRfinder	% of Denoeud VNTRs called by VNTRfinder as variant or non-variant	% of Denoeud non-variants called by VNTRfinder as variant or non-variant
Denoeud v. 40, 10, all variants					Denoeud v. 40, 10, all variants
total repeats matched	10860	86.59			total repeats matched	3533	82.18
DEN⁺, VNTRfinder⁺ *	72		94.7		DEN⁺, VNTRfinder⁺	69		81.2
DEN⁺, VNTRfinder^-	4		5.3		DEN⁺, VNTRfinder^-	16		18.8
DEN^-, VNTRfinder⁺	0			0	DEN^-, VNTRfinder⁺	2			0
DEN^-, VNTRfinder^-	10784			100	DEN^-, VNTRfinder^-	3446			100
Denoeud v. 40, 10, multiple of unit					Denoeud v. 40, 10, multiple of unit
total repeats matched	10160	81.01			total repeats matched	1615	37.57
DEN⁺, VNTRfinder⁺	39		92.9		DEN⁺, VNTRfinder⁺	9		75.0
DEN⁺, VNTRfinder^-	3		7.1		DEN⁺, VNTRfinder^-	3		25.0
DEN^-, VNTRfinder⁺	0			0	DEN^-, VNTRfinder⁺	0			0
DEN^-, VNTRfinder^-	10118			100	DEN^-, VNTRfinder^-	1603			100

* '+/-' indicate repeats reported as variants/non-variants.
Repeats were matched between the results reported by VNTRfinder and those reported by the method of Denoeud and Vergnaud.

ISSN: 1471-2164