Proceedings Article10.1145/279069.279104
Algorithms for optical mapping
Richard M. Karp,Ron Shamir +1 more
- 01 Mar 1998
- pp 117-124
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TL;DR: This paper studies the problem of constructing a restriction map based on optical mapping data and gives several variants of a polynomial reconstruction algorithm, as well as an algorithm that is exponential in the number of cut sites, and hence is appropriate only for small number of Cut sites.
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Abstract: Optical mapping is a novel technique for determining the restriction sites on a DNA molecule by directly observing a number of partially digested copies of the molecule under a light microscope. The problem is complicated by uncertainty as to the orientation of the molecules and by erroneous detection of cuts. In this paper we study the problem of constructing a restriction map based on optical mapping data. We give several variants of a polynomial reconstruction algorithm, as well as an algorithm that is exponential in the number of cut sites, and hence is appropriate only for small number of cut sites. We give a simple probabilistic model for data generation and for the errors and prove probabilistic upper and lower bounds on the number of molecules needed by each algorithm in order to obtain a correct map, expressed as a function of the number of cut sites and the error parameters. To the best of our knowledge, this is the first probabilistic analysis of algorithms for the problem. We also provide expe...
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Citations
Patent
System and process for validating, aligning and reordering one or more genetic sequence maps using at least one ordered restriction map
Marco Antoniotti,Bhubaneswar Mishra,Thomas Anantharaman,Salvatore Paxia,David C. Schwartz +4 more
- 28 Sep 2001
TL;DR: In this paper, a method and system for comparing ordered segments of a first DNA restriction map with ordered segment of a second DNA restriction maps to determine a level of accuracy the first DNA map and/or the second DNA map.
25
A new approach to protein identification
Nuno Bandeira,Dekel Tsur,Ari Frank,Pavel A. Pevzner +3 more
- 02 Apr 2006
TL;DR: The MS/MS database search is reduced to extremely fast pattern matching (rather than time-consuming matching of spectra against databases), and the approach provides a new paradigm for identifying post-translational modifications.
Combinatorial optimization in DNA mapping — a computational thread of the Simplified Partial Digest Problem
Jacek Blazewicz,Marta Kasprzak +1 more
TL;DR: The new approach to the genome mapping of DNA molecules — the Simplified Partial Digest Problem (SPDP), is analyzed and is proved to be strongly NP-hard for the general error-free case.
Partitioning single-molecule maps into multiple populations: algorithms and probabilistic analysis
Laxmi Parida,Bud Mishra +1 more
TL;DR: A complete computational complexity analysis of the “ K -populations” problem along with a probabilistic analysis is provided and some simple polynomial heuristics are presented, while exposing the relations among various error sources that the optical mapping approach may need to cope with.
7
References
Probability Inequalities for sums of Bounded Random Variables
TL;DR: In this article, upper bounds for the probability that the sum S of n independent random variables exceeds its mean ES by a positive number nt are derived for certain sums of dependent random variables such as U statistics.
Probability Inequalities for Sums of Bounded Random Variables
N. I. Fisher,Pranab Kumar Sen +1 more
- 01 Jan 1994
TL;DR: In this article, the Bienayme-Chebyshev inequality for random variables with finite rnean and variance was shown to hold for n independent, identically distributed random variables.
3.2K
The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library.
TL;DR: The strategy was to measure the sizes of partial restriction enzyme digests by hybridization with a vector probe in a manner analogous to nucleotide sequencing, and found that this strategy is applicable to analyses of the genomes of other organisms.
1.8K