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Figure 7 | Algorithms for Molecular Biology

Figure 7

From: Unrooted unordered homeomorphic subtree alignment of RNA trees

Figure 7

The incorporation of cavity matching subroutines in the DP algorithm. (a) Upon reaching the entry corresponding to T u v 1 and S u v 2 , all values of the form Rooted-HSA - r ( T v j u , S v j u ) for v j N(u)  {v1} and v j N( u ) are computed (see (b)). This allows to compute all valuesMCM(N(u){ v 1 },N( u ){ v j }, w u , u v 1 , v j ), by solving the All-Cavity-MCM problem over the instance(N(u){ v 1 },N( u ), w u , u v 1 ), and thus computing term III with respect to all remaining entries in the first row of H u , u . (c) Upon reaching the entry corresponding to T u v 2 and S u v 2 , all values of the form Rooted-HSA - r ( T v j u , S v j u ) for v j N(u) and v j N( u ) are computed (see (d)). This allows to compute all valuesMCM(N(u){ v j },N( u ){ v j }, w u , u v j , v j ), by solving the All-Pairs-Cavity-MCM problem over the instance(N(u),N( u ), w u , u ), and thus computing term III with respect to all remaining entries in H u , u .

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