Tools for the identification of variable and potentially variable tandem repeats

BMC Genomics

Table 1 Repeats detected in strains of Mycobacterium tuberculosis and Neisseria meningitidis.

	Method*	Total**	Number of variants detected
Total repeats detect by TRF in *Mycobacterium tuberculosis* CDC1551		19411
	Denoeud	12542	130
Repeats matched to *Mycobacterium tuberculosis* H37Rv	VNTRfinder (40, 10, all variants)	15964	116
	VNTRfinder (40, 10, multiple of unit)	14490	61
Total repeats detect by TRF in *Neisseria meningitidis* MC58		8419
	Denoeud	4299	173
	VNTRfinder (40, 10, all variants)	5807	177
Repeats matched to *Neisseria meningitidis* Z2491	VNTRfinder (40, 10, multiple of unit)	2504	22
	VNTRfinder (20, 4, all variants)	5822	174
	VNTRfinder (20, 4, multiple of unit)	2516	21
	VNTRfinder (10, 2, all variants)	5382	301
	VNTRfinder (10, 2, multiple of unit)	2338	9

* VNTRfinder settings are given respectively in parentheses as the flanklength allowed, mismatch allowed, and whether or not repeat length differences from the query were required to be multiples of the tandem repeat unit.
** Totals shown are those that align perfectly with the flanks of a repeat originally reported by TRF.
Proportions of total repeats originally detected in Neisseria meningitidis MC58 and Mycobacterium tuberculosis CDC1551 that were successfully matched by the different methods to Neisseria meningitidis Z2491 and Mycobacterium tuberculosis H37Rv respectively. 'all variants' refers to the VNTRfinder option to report any detected variation and 'multiple of unit' refers to the option to only report variations where the length variation is consistent with a change in the repeat copy-number. The number of variants detected is also highlighted.

ISSN: 1471-2164