Using affinity propagation for identifying subspecies among clonal organisms: lessons from M. tuberculosis

BMC Bioinformatics

Table 2 Assignations of LAM7, H4 and selected "U" spoligotype patterns from SpolDB4, according to different methods.

	SpolDB4		Recent litterature	Deletions	Domain Walls	SpotClust subfamily
SIT	family	Sub-family	assignation	family	family	SpolDB3-based	RIM
41	LAM	LAM7	T-TUR	T	LAM	LAM9	N19
186	LAM	LAM7	T-TUR	T	LAM	LAM9	N19
367	LAM	LAM7	T-TUR	T	LAM	LAM9	N19
930	LAM	LAM7	T-TUR	T	LAM	LAM1	N19
1261	LAM	LAM7	T-TUR	T	LAM	LAM9	N19
1589	LAM	LAM7	T-TUR	T	LAM	LAM3	N2
1924	LAM	LAM7	T-TUR	T	LAM	LAM9	N19
1937	LAM	LAM7	T-TUR	T	LAM	LAM9	N19
35	H	H4	T-Ural	T	H	H3	N34
262	H	H4	T-Ural	T	H	H3	N34
361	H	H4	T-Ural	T	H	H3	N34
399	H	H4	T-Ural	T	H	T2	N34
596	H	H4	T-Ural	T	H	H3	N34
597	H	H4	T-Ural	T	H	H3	N34
656	H	H4	T-Ural	T	H	H3	N34
762	H	H4	T-Ural	T	H	H3	N34
777	H	H4	T-Ural	T	H	H3	N34
817	H	H4	T-Ural	T	H	H3	N34
920	H	H4	T-Ural	T	H	H3	N34
921	H	H4	T-Ural	T	H	H3	N34
922	H	H4	T-Ural	T	H	H3	N34
1117	H	H4	T-Ural	T	H	H3	N34
1134	H	H4	T-Ural	T	H	H3	N34
1165	H	H4	T-Ural	T	H	H3	N34
1174	H	H4	T-Ural	T	H	H3	N34
1242	H	H4	T-Ural	T	H	U	N34
1269	H	H4	T-Ural	T	H	H3	N34
1276	H	H4	T-Ural	T	H	H3	N34
1281	H	H4	T-Ural	T	H	H3	N34
1292	H	H4	T-Ural	T	H	H3	N34
1447	H	H4	T-Ural	T	H	H3	N34
1448	H	H4	T-Ural	T	H	H3	N34
1457	H	H4	T-Ural	T	H	H3	N34
1568	H	H4	T-Ural	T	H	H3	N34
1581	H	H4	T-Ural	T	H	H3	N34
1384	H	H4	T-Ural	T	U	T3	N40
1446	H	H4	T-Ural	T	U	H3	N34
1452	H	H4	T-Ural	T	U	H3	N34
1455	H	H4	T-Ural	T	U	U	N34
1456	H	H4	T-Ural	T	U	H3	N34
1461	H	H4	T-Ural	T	U	H3	N34
1480	H	H4	T-Ural	T	U	LAM9	N19
105	U	U	H	U	Afri	LAM7	N29
1274	U	U	LAM	U	Afri	H1	N5
1531	U	U	X	X	X	X1	N44

"Recent literature assignation" represents the standard, and refers to studies using loci other than the CRISPR locus: T-TUR classification has been suggested both by Millet et al. [35] and Abadia et al. [34] based respectively on VNTR signature and SNPs signatures. T-Ural classification has been suggested by Kovalev et al. [36] as they clustered with H37Rv strains and Abadia et al. [34]. RIM: Randomly Initialized Model. N ... families as defined by Spotclust are described on their web-site based on what SpolDB4 families/sub-families are mostly represented: N2 family is described as LAM3-rich; N5 as H1-rich; N19 as LAM-rich; N29 as LAM+EAI-rich; N34 as H3+S-rich; N40 as T3-africanum-rich; N4 as X1-H37Rv-rich. The assignations matching the standard are shown in bold characters. Assignations failures are shown in italic. Note that the "Deletions" method provides the highest number of exact assignations and the least assignation failures.

ISSN: 1471-2105