Combinatorial algorithms for integrated circuit layout
Combinatorial algorithms for integrated circuit layout
On constructing radiation hybrid maps (extended abstract)
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
An algorithmic approach to multiple complete digest mapping
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
Algorithms for computing and integrating physical maps using unique probes
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
Building human genome maps with radiation hybrids
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
Beyond islands (extended abstract): runs in clone-probe matrices
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
Algorithms for optical mapping
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Construction of physical maps from oligonucleotide fingerprints data
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Mapping clones with a given ordering or interleaving
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
Physical mapping of chromosomes using unique probes
SODA '94 Proceedings of the fifth annual ACM-SIAM symposium on Discrete algorithms
A Geometric Approach to Betweenness
ESA '95 Proceedings of the Third Annual European Symposium on Algorithms
Parallel Monte Carlo Methods for Physical Mapping of Chromosones
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
A Parallel Genetic Algorithm for Physical Mapping of Chromosomes
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
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We present 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. In this protocol, which is simple, inexpensive, and has been used to successfully map several organisms, equal-length clones are hybridized against a clone-subset called the probes. The probes are chosen by a sequential process that is designed to generate a pairwise-nonoverlapping subset of the clones. We derive a likelihood function on probe spacings and orders for this protocol under a natural model of hybridization error, and describe how to reconstruct the most likely spacing for a given order under this objective using continuous optimization. The approach is tested on simulated data and real data from chromosome VI of Aspergillus nidulans. On simulated data we recover the true order and close to the true spacing; on the real data, for which the true order and spacing is unknown, we recover a probe order differing significantly from the published one. To our knowledge this is the first practical approach for computing a globally-optimal maximum-likelihood reconstruction of interprobe distances from clone-probe hybridization data.