EGNAS: an exhaustive DNA sequence design algorithm

BMC Bioinformatics

Table 5 Calculations with included sequences to design additional 15 bases long sequences

No.	ΔG	Faulhammer	ΔG	Feldkamp	ΔG	EGNAS
	$[\frac{kcal}{mol}]$	5’ → 3’	$[\frac{kcal}{mol}]$		$[\frac{kcal}{mol}]$	5’ → 3’
1	*	ATCCTCCACTTCACA	*	CTTCTCTCACCTATA	*	CCTACAAATCAACTC
2	*	CTATTTCTCCACACC	*	GGCAAGAGGAATAAT	*	CTAAACACATCCAAC
3	*	CACCCTTTCTCCTCT	2.0	GCGAAAATTAACTCC	*	GCAGAACAAGATAAG
4	*	TCCTCACATTACTTA	1.9	GATCCGGTTACTAAA	*	CCTTCACTTACATTC
5	*	ACTTCCTTTATATCC	1.9	ACCTGACTCGTAATA	*	CTCTCACAATCTAAC
6	*	TCCACCAACTACCTA	1.6	TAAGTATATCGTGCC	*	CAATTTAACCTCCTC
7	2.6	AACTCTCAAATTCAA	1.6	GTCTGAGCTGATAAA	*	CTTCCATATACACTC
8	2.6	ACCTTACTTTCCATA	1.5	GTACCGTTGAATTGT	*	CCACACCTTAATATC
9	2.1	CTCTTACTCAATTCT	1.2	TGCGACTATGTTATG	*	CTATAATTCTCCACC
10	2.1	GTACATTCTCCCTAC	1.1	TTACAGCGTTTTACC	2.8	CGTTGTCTCTATTTC
11	1.8	TTATAACAAACATCC	1.0	AAAGCCGTCAAATAC	2.6	GTTCAGTATTCGTTC
12	1.8	TTTTAAATTTCACAA	1.0	TACCTTTTTGTCTCG	2.5	GTAGCGAAGAAAATG
13	1.6	ATAATCACATACTTC	0.8	ACAGGCGTATCTAAT	2.5	GGTTGCGTTTTATTG
14	1.6	CATTCCTTATCCCAC	0.4	AGTGACACTAGCATT	2.5	CATCGTCAAGTAAAG
15	1.4	CATATCAACATCTTA	0.4	ATGAGGCAGTCTTTA	2.5	CTTTGGTCTGTTATG
16	1.4	TTAAAATCTTCCCTC	0.2	AAGCTATTGATTGGC	2.2	GTCTTTTTGCTTTCG
17	1.3	CTAACCTTTACTTCA	0.1	CACTTGAGTACAACA	2.2	GCAGTTTCATAGTTC
18	1.2	GCTTCAAACAATTCC	0.1	GGATGTCCTTGTTTA	2.0	CTTCTACTACCTATC
19	1.2	ACATAACCCTCTTCA	-0.3	ACCAAACCATGATGA	1.9	GATTAGTGGTTTGAG
20	0.1	CATAATCTTATATTC	-0.7	TGGTAGGCCATTTAA	1.8	CTCATCATTACCATC
				#		#
						GC ends
L _c		8		5		5
L _hp		5		5		3
L _sc		8		6		6
L _sl		5		5		5

Comparison of 15 bases long sequences generated by Faulhammer et al.[14], Feldkamp et al.[20] and EGNAS. Molar free enthalpies of the most stable hairpins.
^*No hairpin structure possible.
^#Without {GGG;CCC}.

ISSN: 1471-2105