Validation of S. Pombe sequence assembly by microarray hybridization

West, J., Healy, J., Wigler, M. H., Casey, W., Mishra, B. (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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URL: https://www.ncbi.nlm.nih.gov/pubmed/16472019
DOI: 10.1089/cmb.2006.13.1

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:
Communities: CSHL labs > Wigler lab
Depositing User: CSHL Librarian
Date Deposited: 08 Dec 2011 15:12
Last Modified: 07 Nov 2016 20:42
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22931

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