Detecting epigenetic motifs in low coverage and metagenomics settings

BMC Bioinformatics

Table 1 Previously identified motifs

Species	Motif	% Modified	Study
E. coli	G ^m6ATC	94.1	Fang 2012
E. coli	ACC ^m6ACC	93.2	Fang 2012
E. coli	CTGC^m6AG	96.3	Fang 2012
G. metallireducens	G ^m6ATCC	99.2	Murray 2012
G. metallireducens	GG ^m6ATC	98.7	Murray 2012
G. metallireducens	TCC ^m6AGG	98.2	Murray 2012
B. Cereus ATCC 10987	CGA ^m6AG	93.3	Murray 2012
B. Cereus ATCC 10987	A ^m4CGGC	33.8	Murray 2012
B. Cereus ATCC 10987	TGC ^m4CG	47.5	Murray 2012
C. Jejuni 81-176	RA ^m6ATTY	99.0	Murray 2012
C. Jejuni 81-176	GCA ^m6AGG	97.7	Murray 2012
C. Jejuni 81-176	GGRC ^m6A	97.6	Murray 2012
C. Jejuni NCTC 11168	RA ^m6ATTY	99.2	Murray 2012
C. Jejuni NCTC 11168	GKA ^m6AYG	98.2	Murray 2012
C. Salexigens	RG ^m6ATCY	76.5	Murray 2012

Motifs from previous studies [3, 4] used to validate the new method. Degenerate bases are identified via corresponding IUPAC symbols. The "RG ^m6ATCY" motif consensus corresponds to 4 distinct motifs.

ISSN: 1471-2105