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ODS: ordering DNA sequences--a physical mapping algorithm based on simulated annealing

A J Cuticchia1, J Arnold, W E Timberlake

  • 1Johns Hopkins School of Medicine, Baltimore, MD 21205.

Computer Applications in the Biosciences : CABIOS
|April 1, 1993
PubMed
Summary
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The ODS program rapidly orders random clones for physical mapping using binary signatures from oligonucleotide probes. This method efficiently reconstructs chromosomes by analyzing clone overlap and is versatile for various data types.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Physical mapping is crucial for understanding genome organization and function.
  • Existing methods for ordering DNA clones can be computationally intensive and data-specific.

Purpose of the Study:

  • To introduce the ODS program, a novel methodology for rapid physical map construction.
  • To present a versatile approach for ordering random clones based on binary signature similarity.

Main Methods:

  • Assigning binary signatures to each clone by hybridizing with oligonucleotide probes.
  • Utilizing the similarity of binary signatures to infer clone overlap and order.
  • Reconstructing the physical map by minimizing the sum of linking distances between ordered clones.

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Main Results:

  • The ODS program offers a fast and efficient method for ordering random clones.
  • Demonstrated versatility in utilizing various presence-absence data types for chromosome reconstruction.
  • Achieved computational efficiency, requiring only hours on standard workstations for large maps.

Conclusions:

  • ODS provides a generalized and computationally efficient solution for physical map construction.
  • The methodology's flexibility accommodates diverse genetic data, enhancing its applicability.
  • This approach significantly accelerates the process of creating high-resolution physical maps.