In the context of comparative analysis of protein–protein interaction graphs, we use a graph-based formalism to detect the preservation of a given protein complex (pattern graph) in the protein–protein interaction graph (target graph) of another species with respect to (w.r.t.) orthologous proteins. We give an efficient exponential-time randomized algorithm in case the occurrence of the pattern graph in the target graph is required to be exact. For approximate occurrences, we prove a tight inapproximability result and give four approximation algorithms that deal with bounded degree graphs, small ortholog numbers, linear forests and very simple yet hard instances, respectively.
Finding common structured patterns in linear graphs.
RIZZI, ROMEO;
2010-01-01
Abstract
In the context of comparative analysis of protein–protein interaction graphs, we use a graph-based formalism to detect the preservation of a given protein complex (pattern graph) in the protein–protein interaction graph (target graph) of another species with respect to (w.r.t.) orthologous proteins. We give an efficient exponential-time randomized algorithm in case the occurrence of the pattern graph in the target graph is required to be exact. For approximate occurrences, we prove a tight inapproximability result and give four approximation algorithms that deal with bounded degree graphs, small ortholog numbers, linear forests and very simple yet hard instances, respectively.
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