Physical mapping of chromosomes using unique probes

@article{Alizadeh1994PhysicalMO,
  title={Physical mapping of chromosomes using unique probes},
  author={Farid Alizadeh and Richard M. Karp and Deborah K. Weisser and Geoffrey Zweig},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  year={1994},
  volume={2 2},
  pages={
          159-84
        }
}
  • F. AlizadehR. Karp G. Zweig
  • Published 23 January 1994
  • Computer Science
  • Journal of computational biology : a journal of computational molecular cell biology
The goal of physical mapping of the genome is to reconstruct a strand of DNA given a collection of overlapping fragments, or clones, from the strand. We present several algorithms to infer how the clones overlap, given data about each clone. We focus on data used to map human chromosomes 21 and Y, in which relatively short substrings, or probes, are extracted from the ends of clones. The substrings are long enough to be unique with high probability. The data we are given is an incidence matrix… 
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Highly Influential Citations
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125 Citations

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This work presents a new method for reconstructing the distances between probes in physical maps of chromosomes constructed by hybridizing pairs of clones under the so-called sampling-without-replacement protocol, and is the first practical approach for computing a globally-optimal maximum-likelihood reconstruction of interprobe distances from clone-probe hybridization data.

Reconstructing Order and Distance in Physical Maps Using Nonoverlapping Probes

We present a new method for reconstructing both the order and spacing of probes in physical maps of chromosomes constructed by hybridizing pairs of clones under the so-called…

Creating Physical Maps With Automatic Capture of Hybridization Data

Several methods for creating physical maps with the automatic capture of data are examined, including one method hybridization data is scored by software using a threshold, and a novel approach using raw levels of hybridization are used by a novel physical mapping algorithm.

Beyond Islands: Runs in clone-probe matrices

This paper analyzes the distribution of {open_quotes}runs{close_qu quotes} - groups of probes whose relative order is completely determined by the hybridization experiment, and includes analytic, numerical, Monte Carlo, and simulation results on runs, which can further assist in the design of these experiments.

Beyond islands (extended abstract): runs in clone-probe matrices

This paper analyzes the distribution of “runs” groups of probes whose relative order is completely determined by the hybridization experiment, and includes analytic, numerical, Monte Carlo, and simulation results on runs, which can further assist in the design of these experiments.

Beyond Islands : Runs in Clone-Probe Matrices ( extended abstract )

Physical mapping is a fundamental component of the human genome project. A physical map consists of a set of probes which mark unique positions on a long fragment of DNA, together with the relative…

Placing Probes along the Genome Using Pairwise Distance Data

The theoretical basis of an approach using microarrays of probes and libraries of BACs to construct maps of the probes, by assigning relative locations to the probes along the genome is described, and an efficient approximation algorithm is developed.

Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut

We introduce a new combinatorial formulation of chromosome physical-mapping by the sampling-without-replacement protocol. In this protocol, which is simple, inexpensive, and has been used to…

Efficient Methods for Determining DNA Probe Orders

A measure of such imperfectness of the data is defined as the minimum amount of the additional fragments that are needed to uniquely fix the probe order in STS-based mapping.

Imperfectness of Data for STS-Based Physical Mapping

A measure of such imperfectness of the data is defined as a minimum amount of additional fragments which are needed to fix the probe order uniquely and several polynomial-time algorithms to compute such additional fragments of minimum cost are presented.
...

19 References

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

The program ODS is very general in the types of data that can be utilized for chromosome reconstruction, such as hybridized synthetic oligonucleotides, restriction endonuclease recognition sites or single copy landmarks, can be used for analysis.

Optimized strategies for sequence-tagged-site selection in genome mapping.

The results of these simulations suggest that a nonrandom STS strategy that uses paired probes requires one-third to one-fourth as many STS assays as are required in random and nonpaired approaches, and also results in a map that has both greater genome coverage and a larger average contig size.

The human Y chromosome: overlapping DNA clones spanning the euchromatic region.

The human Y chromosome was physically mapped by assembling 196 recombinant DNA clones, each containing a segment of the chromosome, into a single overlapping array, revealing that Y-chromosomal genes are scattered among a patchwork of X-homologous, Y-specific repetitive, and single-copy DNA sequences.

Physical mapping of chromosomes: A combinatorial problem in molecular biology

Combinatorial algorithms are presented for solving approximations to the physical mapping of DNA molecules using data about the hybridization of oligonucleotide probes to a library of clones.

The Chimeric Mapping Problem: Algorithmic Strategies and Performance Evaluation on Synthetic Genomic Data

Algorithms and software tools for ordering clone libraries: application to the mapping of the genome of Schizosaccharomyces pombe.

A complete set of software tools to aid the physical mapping of a genome has been developed and successfully applied to the genomic mapping of the fission yeast Schizosaccharomyces pombe. Two…

A 13 kb resolution cosmid map of the 14 Mb fission yeast genome by nonrandom sequence-tagged site mapping

An algorithm to detect chimeric clones and random noise in genomic mapping.

An algorithm is described that easily identifies false positive signals and clones containing chimeric inserts/internal deletions and "dechimerizes" clones, splitting them into independent contiguous components and cleaning the initial library into a more consistent data set for further ordering.

The human Y chromosome: a 43-interval map based on naturally occurring deletions.

A deletion map of the human Y chromosome was constructed by testing 96 individuals with partial Y chromosomes for the presence or absence of many DNA loci, and should be useful in identifying Y chromosomal genes, in exploring the origin of chromosomal disorders, and in tracing the evolution of the Y chromosome.

A fast random cost algorithm for physical mapping.

A physical mapping algorithm for creating ordered genomic libraries or contig maps by using a random cost approach that is 5-10 times faster than existing physical mapping algorithms and has optimization performance comparable to existing procedures.