Abstract
We study the Partial Information Network Query (PINQ) problem, which generalizes two problems that often arise in bioinformatics: the Alignment Network Query (ANQ) problem and the Topology-Free Network Query (TFNQ) problem. In both ANQ and TFNQ we have a pattern P and a graph H, and we seek a subgraph of H that resembles P. ANQ requires knowing the topology of P, while TFNQ ignores it. PINQ fits the scenario where partial information is available on the topology of P. Our main result is a parameterized algorithm that handles inputs for PINQ in which P is a set of trees. This algorithm significantly improves the best known O∗ running time in solving TFNQ. We also improve the best known O∗ running times in solving two special cases of ANQ.
Original language | English |
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Pages (from-to) | 129-145 |
Number of pages | 17 |
Journal | Journal of Discrete Algorithms |
Volume | 31 |
DOIs | |
State | Published - 1 Mar 2015 |
Externally published | Yes |
Keywords
- Alignment network query
- Parameterized algorithm
- Partial information network query
- Pattern matching
- Topology-free network query
ASJC Scopus subject areas
- Theoretical Computer Science
- Discrete Mathematics and Combinatorics
- Computational Theory and Mathematics