Research on Pattern Matching with Wildcards and Length Constraints: Methods and Completeness

Wang, Haiping; Xiang, Taining; Hu, Xuegang

doi:10.5772/48574

Cited by 2 publications

(2 citation statements)

References 24 publications

(18 reference statements)

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“…All of these algorithms are randomized. We note that there are several problems related to ANQ that have applications in bioinformatics, and refer the reader to the surveys [2,17] for the precise details. The Topology-Free Network Query Problem: Unweighted TFNQ (i.e., TFNQ restricted to inputs in which all the edge-weights are 0) was introduced by Lacroix et al [18], and TFNQ was introduced by Bruckner et al [19].…”

Section: Prior Workmentioning

confidence: 99%

Partial Information Network Queries

Pinter

Shachnai

Zehavi

2015

Journal of Discrete Algorithms

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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.Keywords: parameterized algorithm, pattern matching, partial information network query, alignment network query, topology-free network query

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Section: Prior Workmentioning

confidence: 99%

Partial Information Network Queries

Pinter

Shachnai

Zehavi

2015

Journal of Discrete Algorithms

View full text Add to dashboard Cite

show abstract

“…We note that there are several problems related to ANQ that have applications in bioinformatics, and refer the reader to the surveys [2,17] for the precise details. The Topology-Free Network Query Problem: Unweighted TFNQ (i.e., TFNQ restricted to inputs in which all the edge-weights are 0) was introduced by Lacroix et al [18], and TFNQ was introduced by Bruckner et al [19].…”

Section: Prior Workmentioning

confidence: 99%