Partitioning single-molecule maps into multiple populations

Algorithms and probabilistic analysis

Laxmi Parida, Bud Mishra

Research output: Contribution to journalArticle

Abstract

Given a set of m molecules, derived from K homologous clones, we wish to partition these molecules into K populations, each giving rise to distinct ordered restriction maps, thus providing simple means for studying biological variations. With the emergence of single-molecule methods, such as optical mapping, that can create individual ordered restriction maps reliably and with high throughput, it becomes interesting to study the related algorithmic problems. In particular, we provide a complete computational complexity analysis of the "K-populations" problem along with a probabilistic analysis. We also present some simple polynomial heuristics, while exposing the relations among various error sources that the optical mapping approach may need to cope with. We believe that these results will be of interest to computational biologists in devising better algorithms, to biochemists in understanding the trade-offs among the error sources and finally, to biologists in creating reliable protocols for population study.

Original languageEnglish (US)
Pages (from-to)203-227
Number of pages25
JournalDiscrete Applied Mathematics
Volume104
Issue number1-3
StatePublished - Aug 15 2000

Fingerprint

Algorithm Analysis
Probabilistic Analysis
Partitioning
Molecules
Restriction
Complexity Analysis
Computational Analysis
Computational complexity
Clone
Throughput
Polynomials
High Throughput
Network protocols
Computational Complexity
Trade-offs
Partition
Heuristics
Distinct
Polynomial

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Applied Mathematics
  • Discrete Mathematics and Combinatorics
  • Theoretical Computer Science

Cite this

Partitioning single-molecule maps into multiple populations : Algorithms and probabilistic analysis. / Parida, Laxmi; Mishra, Bud.

In: Discrete Applied Mathematics, Vol. 104, No. 1-3, 15.08.2000, p. 203-227.

Research output: Contribution to journalArticle

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