Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem

Authors:
Serafim Batzoglou;Sorin Istrail
Affiliations:
-;-
Venue:
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
Year:
1999

Citing 4
Cited 0

The traveling salesman problem with distances one and two

Mathematics of Operations Research
Mapping the genome: some combinatorial problems arising in molecular biology

STOC '93 Proceedings of the twenty-fifth annual ACM symposium on Theory of computing
Consecutive storage of relevant records with redundancy

Communications of the ACM
Testing for the consecutive ones property, interval graphs, and graph planarity using PQ-tree algorithms

Journal of Computer and System Sciences

Quantified Score

Hi-index	0.00

Visualization

Abstract

We focus on the combinatorial analysis of physical mapping with repeated probes. We present computational complexity results, and we describe and analyze an algorithmic strategy. We are following the research avenue proposed by Karp [9] on modeling the problem as a combinatorial problem - the Hypergraph Superstring Problem - intimately related to the Lander-Waterman stochastic model [16]. We show that a sparse version of the problem is MAXSNP-complete, a result that carries over to the general case. We show that the minimum Sperner decomposition of a set collection, a problem that is related to the Hypergraph Superstring problem, is NP-complete. Finally we show that the Generalized Hypergraph Superstring Problem is also MAXSNP-hard.We present an efficient algorithm for retrieving the PQ-tree of optimal zero repetition solutions, that provides a constant approximation to the optimal solution on sparse data. We provide experimental results on simulated data.