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Fig. 2 | Algorithms for Molecular Biology

Fig. 2

From: The energy-spectrum of bicompatible sequences

Fig. 2

From two secondary structures to a topological space: A two secondary structures drawn in the upper- and lower-half plan respectively. A rainbow arc (0, 9) is added to both of the structures to close to exterior loop. B The secondary structures are decomposed into loops. The loops induce a hyper-graph \(G=(V=\{0,\ldots , 9\},E)\), where \(E=\{e_1,e_2,e_3,e_4,e_5, e_6\}\) with \(e_1=\{0,1,4,5,7,8,9\},\,e_2=\{1,2,3,4\},\, e_3=\{2,3\},\,e_4=\{5,6,7\}\), \(\,e_5=\{0,1,2,3,4,5,6,8,9\}\) and \(e_6=\{6,7,8\}\) are loops. C The nerve over E. A \((d-1)\)-simplex represent the nontrivial intersection of d loops. D The topological quotient space K(R) induced by C, where a ribbon induced by \(\{e_1, e_2, e_5, e_3\}\) is glued to a sphere induced by \(\{e_1, e_5, e_4, e_6 \}\)

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