G. Mayraz and R. Shamir. Construction of physical maps from oligonucleotide fingerprints data. Journal of Computational Biology, 6(2):237--252. Home/Search Document Details and Download
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Reconstructing Distances in Physical Maps of Chromosomes .. - Kececioglu, Shete.. (Correct)
....sites that are identified by short, uniquely occurring sequences, or positions of clones that contain fragments of the chromosome. There is a diverse array of approaches for constructing maps of such features depending on the type of data that is collected, including mapping by nonunique probes [2, 18], mapping by unique probes [1, 11, 12] mapping by unique endprobes [7] mapping by nonoverlapping probes [8] mapping from restriction fragment length data [10, 13] radiation hybrid mapping [24, 5] and optical mapping [21, 14, 16] there are many probabilistic analyses of various approaches ....
.... length data [10, 13] radiation hybrid mapping [24, 5] and optical mapping [21, 14, 16] there are many probabilistic analyses of various approaches [15, 4, 28, 27, 26] and a wide variety of computational techniques have been employed or suggested, including greedy algorithms [18], simulated annealing [20, 25, 2, 1] linear programming [7, 12, 8] and semidefinite programming [6] In this paper we develop a maximum likelihood approach for a type of physical mapping known as the samplingwithout replacement protocol. The protocol is inexpensive, simple to carry out in the ....
Mayraz, G. and R. Shamir. "Construction of physical maps from oligonucleotide fingerprint data." Proceedings of the 3rd ACM Conference on Computational Molecular Biology, 268--277, 1999.
Algorithms for Molecular Biology Fall Semester, 2001 - Lecture January Lecturer Self-citation (Shamir) (Correct)
....along the genome is a solution to the mapping problem. According to Theorem 9.3, with su#cient coverage Aviv Univ. Figure 9.9: Number of islands as a function of genome equivalence and #. Figure 9.10: Islands length as a function of genome equivalence and #. Aviv Univ. Figure 9. 11: Source: [5].Clones and non unique probes. The clones are the horizontal lines. The random occurrences of a single nonunique probe are marked by the dotted vertical lines. Figure 9.12: Source: 5] Physical (good) map example. The short horizontal lines are the clones with their x coordinates corresponding ....
....and #. Figure 9.10: Islands length as a function of genome equivalence and #. Aviv Univ. Figure 9.11: Source: 5] Clones and non unique probes. The clones are the horizontal lines. The random occurrences of a single nonunique probe are marked by the dotted vertical lines. Figure 9. 12: Source: [5].Physical (good) map example. The short horizontal lines are the clones with their x coordinates corresponding to the position on the target genome. The y coordinates correspond to the clone order in the constructed map. Note that each point on the target genome is covered by many clones. Figure ....
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G. Mayraz and R. Shamir. Construction of physical maps from oligonucleotide fingerprints data. Journal of Computational Biology, 6(2):237--252.
An Algorithm for Clustering cDNAs for Gene Expression.. - Hartuv, Schmitt.. (1999) (19 citations) Self-citation (Shamir) (Correct)
....normal distribution with mean = Ca C b 2 and standard deviation oe = C b GammaC a 6 . The number of probes (i.e. oligos) is p. Probes are assumed to occur along a gene with Poisson distribution with rate . This assumption originally was suggested in [23] and was adopted by other researchers [1, 27, 20]. The probability that an oligo occurrence did not register (false negative probability) is ff. False positive hybridizations are assumed to have Poisson distribution with rate fi. All probe occurrences and error events are assumed to be independent. The result of the simulation is an N Theta p ....
....data. The test reported here was the first run of the algorithm on real data where the solution is known. Clearly our simulation results depend on the assumption that all probes have the same rate, which is not satisfied by randomly chosen probes on real gene sequences. However, as was shown in [20] this can be remedied by a judicious choice 5 of probes. The results on the real dataset al..so demonstrate that the effect of this problem is not large. Additional improvements to the algorithm can be achieved by using faster minimum cut algorithm (e.g. 11] and by attempting to find maximal ....
G. Mayraz and R. Shamir. Construction of physical maps from oligonucleotide fingerprints data. In Proceedings of the Third Annual International Conference on Computational Molecular Biology (RECOMB '99). to appear.
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