Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays

BMC Bioinformatics

Table 1 Summary statistics of designed probe sets for several microbial genomes of different sizes

Species	*S. cellulosum*'So ce 56'		*P. gingivalis* W83		*Candidatus* C. ruddii PV
Genome size	Large, 13 Mbp		Medium, 2.34 Mbp		Small, 0.16 Mbp
Probe number (NimbleGen format)	1620 K (12*135 K)		385 K		72 K (4*72 K)
Window size	16		12		5
Min. distance = smallest gap size	4		3		2
Total non-redundant probes	1620000		385000		72000
Total forward strand starts	818857		204991		36069
Total reverse-compl. strand starts	818947		205024		35931
	Gap size	Number	Gap size	Number	Gap size	Number
Probe distribution	4	123253	3	42959	2	24802
	5	66143	4	22608	3	11222
	6	55731	5	21595	4	20978
	7	54928	6	20832	5	9846
	8	62274	7	21503	6	5152
	9	59254	8	25340
	10	63218	9	25927
	11	79015	10	28351
	12	74532	11	39237
	13	78092	12	24979
	14	92854	13	21136
	15	111273	14	19371
	16	78459	15	17735
	17	75716	16	16567
	18	61562	17	17007
	19	57317	18	16602
	20	59414	19	12493
	21	50445	20	10402
	22	47169	21	5371
	23	49842
	24	42842
	25	41557
	26	41786
	27	32553
	28	28835
	29	27753
	30	21987

ISSN: 1471-2105