Efficient oligonucleotide probe selection for pan-genomic tiling arrays

BMC Bioinformatics

Table 1 Genomic sequences included on the Listeria monocytogenes pan-genome tiling array.

Strain	Lineage	Serotype	Bases	Contigs	Genes*	EGD-e %Idy
EGD-e	II	1/2a	2,944,528	1	3,002	100
LO28	II	1/2c	2,910,810	529	5,078	99.3
FSL F2-515	II	1/2a	2,586,267	1,415	NA	98.41
FSL J2-003	II	1/2a	2,878,206	406	4,686	98.22
1/2a F6854	II	1/2a	2,950,285	133	3,028	98.01
FSL N3-165	II	1/2a	2,886,689	33	2,963	97.52
J2818	II	1/2a	2,971,223	38	3,270	97.19
F6900	II	1/2a	2,958,319	35	3,333	97.15
J0161	II	1/2a	3,051,828	51	3,252	97.09
10403S	II	1/2a	2,866,709	32	2,944	96.9
FSL J2-064	I	1/2b	2,899,431	327	3,914	94.69
4b H7858	I	4b	2,972,254	181	3,187	94.54
FSL J1-175	I	1/2b	2,902,346	357	4,559	94.49
FSL N1-017	I	4b	2,857,865	77	3,465	94.3
HPB2262	I	4b	3,006,068	75	3,319	94.01
FSL J1-194	I	1/2b	2,986,227	44	3,792	93.98
4b F2365	I	4b	2,905,187	1	2,987	93.87
FSL R2-503	I	1/2b	3,001,696	54	4,863	93.73
FSL J2-071	IIIA	4c	3,149,923	46	3,789	93.28
FSL J1-208	IIIB	4a	2,260,760	1,494	NA	92.84

Sequences and annotations were obtained from NMPDR. The final column shows the nucleotide identity of a whole-genome alignment versus strain EGD-e. *Number of annotated protein coding genes and RNAs reported by NMPDR at the time of this study.

ISSN: 1471-2105