Constructing maps using the span and inclusion relations

Fasulo, Dan; Jiang, Tao; Karp, Richard M.; Sharma, Nitin

doi:10.1145/279069.279090

Cited by 4 publications

(2 citation statements)

References 9 publications

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“…C(X, Y) holds if interval X contains interval Y, and S(X, Y, Z) holds if interval Z is contained in the union of interval X and interval Y, but neither X nor Y contains Z. A related paper (Fasulo et al, 1998) gives a polynomial-time algorithm for the following interval arrangement problem: given a binary relation C and a ternary relation 5 over a finite set U, determine whether the relations have a realization by intervals, i.e., whether the elements of U can be identified with intervals such that C is the containment relation between intervals and S is the span relation for triples of intervals. If such a realization exists, the algorithm constructs the event sequence of one such realization.…”

Section: Ordering the Clonesmentioning

confidence: 99%

An Algorithmic Approach to Multiple Complete Digest Mapping

Fasulo¹,

Jiang²,

Karp³

et al. 1999

Journal of Computational Biology

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Multiple Complete Digest (MCD) mapping is a method of determining the locations of restriction sites along a target DNA molecule. The resulting restriction map has many potential applications in DNA sequencing and genetics. In this work, we present a heuristic algorithm for fragment identification, a key step in the process of constructing an MCD map. Given measurements of the restriction fragment sizes from one or more complete digestions of each clone in a clone library covering the molecule to be mapped, the algorithm identifies groups of restriction fragments on different clones that correspond to the same region of the target DNA. Once these groups are correctly determined the desired map can be constructed by solving a system of simple linear inequalities. We demonstrate the effectiveness of our algorithm on real data provided by the Genome Center at the University of Washington.

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Section: Ordering the Clonesmentioning

confidence: 99%

An Algorithmic Approach to Multiple Complete Digest Mapping

Fasulo¹,

Jiang²,

Karp³

et al. 1999

Journal of Computational Biology

Self Cite

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“…Chain graphs have also been investigated in [2]. However, the graph-modification problem arising in [2] is different from the ones studied in this paper.…”

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confidence: 96%

Approximating the Minimum Chain Completion problem

Feder¹,

Mannila

Terzi

2009

Information Processing Letters

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A polynomial approximation algorithm for the minimum fill-in problem

Natanzon

Shamir

Sharan

1998

Proceedings of the Thirtieth Annual ACM Symposium on Theory of Computing - STOC '98

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In the minimum fill-in problem, one wishes to find a set of cdgco of smallest size, whose addition to a given graph will make it chordal, The problem has important applications in numerical algebra and has been studied intensively since the 197Os, We give the first polynomial approximation algorithm for the problem, Our algorithm constructs a triangulation whose size is at most eight times the optimum size aquarcd, The algorithm builds on the recent parameterized algorithm of Kaplan, Shamir and Tarjan for the same problem.For bounded degree graphs we give a polynomial approximation algorithm with a polylogarithmic approximation ratio, We also improve the parameterized algorithm.

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Constructing maps using the span and inclusion relations

Abstract: Introduction

Cited by 4 publications

References 9 publications

An Algorithmic Approach to Multiple Complete Digest Mapping

An Algorithmic Approach to Multiple Complete Digest Mapping

Approximating the Minimum Chain Completion problem

A polynomial approximation algorithm for the minimum fill-in problem

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