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Frank Gurski

Publications and source records attributed to Frank Gurski.

20 records · Page 2Linked to original sources

A note on module-composed graphs

In this paper we consider module-composed graphs, i.e. graphs which can be defined by a sequence of one-vertex insertions v_1,...,v_n, such that the neighbourhood of vertex v_i, 2<= i<= n, forms a module (a homogeneous set) of the graph defined by vertices v_1,..., v_{i-1}. We show that module-composed graphs are HHDS-free and thus homogeneously orderable, weakly chordal, and perfect. Every bipartite distance hereditary graph, every (co-2C_4,P_4)-free graph and thus every trivially perfect graph is module-composed. We give an O(|V_G|(|V_G|+|E_G|)) time algorithm to decide whether a given graph G is module-composed and construct a corresponding module-sequence. For the case of bipartite graphs, module-composed graphs are exactly distance hereditary graphs, which implies simple linear time algorithms for their recognition and construction of a corresponding module-sequence.

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Polynomial algorithms for protein similarity search for restricted mRNA structures

In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be NP-complete for planar associated implied structure graphs of vertex degree at most 3. In [BFHV05] a first polynomial dynamic programming algorithms for MRSO on implied structure graphs with maximum vertex degree 3 of bounded cut-width is shown. We give a simple but more general polynomial dynamic programming solution for the MRSO problem for associated implied structure graphs of bounded clique-width. Our result implies that MRSO is polynomial for graphs of bounded tree-width, co-graphs, $P_4$-sparse graphs, and distance hereditary graphs. Further we conclude that the problem of comparing two solutions for MRSO is hard for the class of problems which can be solved in polynomial time with a number of parallel queries to an oracle in NP.

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