Table 3

Avoiding hairpin formation in 20 bases long sequences
No. ΔG TANAKA et al. ΔG FELDKAMP ΔG EGNAS
<a onClick="popup('http://www.biomedcentral.com/1471-2105/13/138/mathml/M7','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/138/mathml/M7">View MathML</a> 5’ → 3’ <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/138/mathml/M8','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/138/mathml/M8">View MathML</a> 5’ → 3’ <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/138/mathml/M9','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/138/mathml/M9">View MathML</a> 5’ → 3’
1 1.1 ATGTACGTGAGATGCAGCAG 1.0 TAGTCGCGTGATTTGGAAGG * GAGAAGGAACACGATACAGC
2 1.1 ATCACTACTCGCTCGTCACT 0.9 GCTGTCTTTCGTCAATACCG * CCTTACACATTTCTTCCGCC
3 0.6 AGATGATCAGCAGCGACACT 0.3 CTGAACGGAATCTAGTAGCG * CACAATCAACTCTACCGCTC
4 0.5 TCTGTACTGCTGACTCGAGT -0.1 GTCTACGGTTCTCTTACGCT 2.4 CCTGTCCTATCTTTCGCTTC
5 0.3 ACATCGACACTACTACGCAC -0.2 AAAGCCGTCGTTTAAGGAGC 2.1 CTGGCTATGGAAACTGAACG
6 -0.2 GCTGACATAGAGTGCGATAC -0.2 AATCGCAGTACAGATGGTGG 1.8 CTCGGTCTAAATCTGCTCTC
7 -0.5 TGTGCTCGTCTCTGCATACT -0.2 GGATGACCAGAGCACTTCAA 1.8 GCCGTTATCCTCTGTTTGTC
8 -0.5 TCAGAGATACTCACGTCACG -0.6 TACGTCTCGAACTGATAGCC 1.8 GGTTTATTGAGGTTGCGAGG
9 -0.8 CGAGTAGTCACACGATGAGA -0.8 TGATCTTGTAAAGGCCAGGC 1.8 CCTCCGTATTTGCCTTGTTG
10 -0.9 CGAGACATCGTGCATATCGT -0.8 TACGATACTTGGCGAGCCAT 1.5 GTTGTAGTTCGTTGGTGGTC
11 -1.2 AGACGAGTCGTACAGTACAG -0.9 TGCAGAAAAACTATGCCGCC 1.5 CTTCGGCTGGTTCTATTCTG
12 -1.8 TATAGCACGAGTGCGCGTAT -1.1 GCGCGGACAATTCATTGGTT 1.4 GGCTCACTCATCACACTAAC
13 -2.2 GATCTACGATCATGAGAGCG -1.7 CCGCAATCCGGTGAAATTAG 1.4 CCTTTACGCCTGACTTTGAC
14 -2.3 GACAGAGCTATCAGCTACTG -3.0 CTTAGGCAGGTGCCACATAT 1.3 CCTGCGTCTTATGTCTCTTG
15 0.9 GCGTGAATGAAGTGGAGTAG
16 0.9 GGATTACTTGCTTGGACTGG
GC ends
# §
Lc 9 5 5
Lhp 5 5 2
Lsc 10 6 4
Lsl 7 5 5

Comparison with TANAKA et al. [17]FELDKAMP et al. [20]. Comparison of 20 bases long sequences generated by TANAKA et al. [17], 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}.

Kick et al.

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

Open Data