EGNAS: an exhaustive DNA sequence design algorithm

BMC Bioinformatics

Table 4 Calculations with included sequences to design additional 20 bases long sequences

No.	ΔG	Arita et al.	ΔG	Feldkamp	EGNAS
	$[\frac{kcal}{mol}]$	5’ → 3’	$[\frac{kcal}{mol}]$		5’ → 3’
1	2.5	CCGTCTTCTTCTGCT	1.5	AAAGCCGTCGTTTCC	GAGAGAAACGGCAAC
2	*	TTCCCTCCCTCTCTT	1.0	TTGTGGTACTCTGCG	CGCAAACTCACCTAC
3	3.0	CGTCCTCCTCTTGTT	1.1	TATTAGATGGCCGCC	GCCTTTACATCTCCG
4	*	CCCCTTCTTGTCCTT	1.3	CTAGCTCCTTTGTCG	CAGAACGACAAAGCC
5	2.5	TGCCCCTCTTGTTCT	0.5	GCATTGTAGTGGCTG	CATACGAAGCACACC
6	*	CTCCTCTTCCTTGCT	-0.5	GGCATATAGCGTGAC	CCAGCCGATAACAAC
7	*	CTTCTCCCTTCCTCT	-0.4	GTTATTGCGACCTCG	GACCAACAGCAAGAC
8	*	CCTTCCTTCCCTCTT	-0.1	AGTCATGGACCAACG	CAAGCGTCATCCAAG
9	2.8	TCCCCTTGTGTGTGT	-2.4	GAACGGTTACCGATC	CACGCCATAAACCAG
10	-1.4	GAGAGAGAGGCCCCCTATCC	-0.6	AAAGACGTGTGAAGTGCGCT	CTACACTCTTCACTTCCACC
11	-2.2	GAAGAGAAGGGCACCCCTCC	-0.9	GACGAAAGTTCAGCAGCGAA	GCCTCATTCTTACCTCCTTC
12	0.6	GTGGTGTTGCGTCCCTTCCC	0.1	TGTTAAAATCAGGCTCGCGC	GAGACCGAAAGATAGCAGAG
13					CAACCGCTCAAATCTACTCC
					GC ends
				#	§
L _c		10		5	5
L _hp		5		5	2
L _sc		6		6	4
L _sl		8		4	5

Comparison of 15 and 20 bases long sequences generated by Arita et al.[13], Feldkamp et al.[20] and EGNAS. Molar free enthalpies of the most stable hairpins.
^*No hairpin structure possible.
^#Without {GGG;CCC}.
^§Without {GGG;CCC;AAAA;TTTT}. For all sequences computed by EGNAS no possible hairpin structures could be found.

ISSN: 1471-2105