Table 2

Avoiding hairpin formation in 22 bases long sequences
No. ΔG FELDKAMP ΔG EGNAS
<a onClick="popup('http://www.biomedcentral.com/1471-2105/13/138/mathml/M5','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/138/mathml/M5">View MathML</a> 5’ → 3’ <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/138/mathml/M6','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/138/mathml/M6">View MathML</a> 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
Lc 5 5
Lhp 5 2
Lsc 6 4
Lsl 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.

Kick et al.

Kick et al. BMC Bioinformatics 2012 13:138   doi:10.1186/1471-2105-13-138

Open Data