EGNAS: an exhaustive DNA sequence design algorithm

BMC Bioinformatics

Table 2 Avoiding hairpin formation in 22 bases long sequences

No.	ΔG	Feldkamp	ΔG	EGNAS
	$[\frac{kcal}{mol}]$	5’ → 3’	$[\frac{kcal}{mol}]$	5’ → 3’
1	-0.3	CCTGCGTCGTTTAAGGAAGTAC	*	GCTCATTTTACACTCTCCACCG
2	0.6	CAGCCAAGATTCTTTTACCGCC	*	CACACGGAGGCACAGAATAAAC
3	0.4	CCATCATGTGTGCCGAGATATG	*	GAACAGCGAAGAGATAGGAAGG
4	0.3	CTTCTCCTAACTGCACGGAATG	*	CCTTACTCGCCTTTCACATTCC
5	-0.3	GGTCCGGTCATAAAGCGATAAG	*	CAACTCACGCCACTACATCAAC
6	0.7	GTCCTCGCCTAGTGTTTCATTG	2.4	CAAGCCGTCAATAGTCCAAGTC
7	0.2	GGATCTGGCGCATAGACAATTC	2.1	CTGCTGAACCTGATACCGAAAC
8	-0.1	CACGTCACTGTTAATCCGAAGC	1.8	CAGTATTTCCAGTCAGTTCCGC
9	-0.1	GTGGAAAGTGGCAATCGTGAAG	1.8	CCTGTCGTTTTCTATGCTCCTG
10	0.6	GGACGAATACAAAGGCTACACG	1.8	CCTGCCGATGACCTACTTTTTG
11	-2.4	CAAGGTCTGCTTGATTTGGAGG	1.6	CCGTTCTTTGTCCTTGCTTCTC
12	-0.9	GTTTTGAACGTAGTAGAGCCGG	1.5	GTGATTGGCTGGTGTTGGTTTG
13	-0.2	GTAGGTGTCGGTGCGAAATTAG	1.3	GCTCGTGGTCTTGTTATGTCTG
14	-0.1	CTAGAACCGTTACGAGTTTGCG	1.1	GTAGATTTGAGGTGCGTTGTGG
L _c		5		5
L _hp		5		2
L _sc		6		4
L _sl		5		5

Comparison with Feldkamp et al.[34]. Comparison of 22 bases long sequences generated by Feldkamp et al.[34] and with EGNAS. The subsequences {GGG;CCC} were forbidden. GC ends were demanded. Molar free enthalpies of the most stable hairpins.
^*No hairpin structure possible.

ISSN: 1471-2105