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.
Complexity issues in color-preserving graph embeddings.
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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