Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA

BMC Genomics

Table 2 Restriction enzymes used for simulations

	Restriction enzyme	Recognition site	Occurrence in RefSeq EST sets (%)
			Arabidopsis thaliana	Homo sapiens	Mus musculus
1	MboI	▼GATC	97.2	98.8	82.5
2	HpaII	C▼CGG	84.4	93.3	64.7
3	HinP1I	G▼CGC	60.3	89.4	61.7
4	Csp6I	G▼TAC	87.9	97.5	81.4
5	TaqI	T▼CGA	95.3	89.4	64.2
6	TasI	▼AATT	97.5	98.2	80.2
7	MseI	T▼TAA	96.3	97.2	78.9
8	FatI	▼CATG	96.4	99.7	83.5
9	MaeI	C▼TAG	88.6	95.1	76.3
10	MaeII	A▼CGT	86.7	92.0	64.8
11	ApoI	R▼AATTY	82.7	86.2	68.5
12	BstYI	R▼GATCY	80.0	90.5	70.4
13	AcyI	GR▼CGYC	37.8	70.3	46.4
14	BmeT110I	CY▼CGRG	49.6	79.3	52.8
15	Cfr10I	R▼CCGGY	49.6	68.6	45.1
16	CfrI	Y▼GGCCR	45.3	90.3	68.7
17	BsaWI	W▼CCGGW	64.1	60.1	44.2
18	TatI	W▼GTACW	63.5	86.8	72.7

All these restriction enzymes are commercially available, supplying companies can be found on the REBASE [23] homepage. Frequency of occurrence in EST sets were calculated using NCBI Reference Sequence collections without repetition, sequences containing more than one copy of a recognition site counted only once.

ISSN: 1471-2164