Validation of S. Pombe sequence assembly by microarray hybridization

West, J., Healy, J., Wigler, M. H., Casey, W., Mishra, B. (January 2006) Validation of S. Pombe sequence assembly by microarray hybridization. J Comput Biol, 13 (1). pp. 1-20. ISSN 1066-5277 (Print)

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Abstract

We describe a method to make physical maps of genomes using correlative hybridization patterns of probes to random pools of BACs. We derive thereby an estimated distance between probes, and then use this estimated distance to order probes. To test the method, we used BAC libraries from Schizzosaccharomyces pombe. We compared our data to the known sequence assembly, in order to assess accuracy. We demonstrate a small number of significant discrepancies between our method and the map derived by sequence assembly. Some of these discrepancies may arise because genome order within a population is not stable; imposing a linear order on a population may not be biologically meaningful.

Item Type:	Paper
Uncontrolled Keywords:	Algorithms Chromosomes Artificial, Bacterial Comparative Genomic Hybridization statistics numerical data Models, Genetic Oligonucleotide Array Sequence Analysis statistics & numerical data Physical Chromosome Mapping statistics & numerical data Schizosaccharomyces genetics Sequence Analysis DNA statistics numerical data
Subjects:	bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function > BAC bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > Mapping and Rendering bioinformatics > genomics and proteomics > annotation > sequence annotation bioinformatics > genomics and proteomics > analysis and processing > Sequence Data Processing bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering bioinformatics > computational biology
CSHL Authors:	Healey, John West, Joseph Wigler, Michael H.
Communities:	CSHL labs > Wigler lab
Depositing User:	CSHL Librarian
Date:	January 2006
Date Deposited:	08 Dec 2011 15:12
Last Modified:	07 Nov 2016 20:42
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/22931

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