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Integrated and sequence-ordered BAC and YAC-based physical maps for the rat genome

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Goesele,  Claaudia
Max Planck Society;

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Himmelbauer,  Heinz
Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society;

Kreitler,  Thomas
Max Planck Society;

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Lehrach,  Hans
Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society;

/persons/resource/persons50666

Zimdahl,  Heike
High Throughput Technologies, Max Planck Institute for Molecular Genetics, Max Planck Society;

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Citation

Krzywinski, M., Wallis, J., Goesele, C., Bosdet, I., Chiu, R., Graves, T., et al. (2004). Integrated and sequence-ordered BAC and YAC-based physical maps for the rat genome. Genome Research, 14(4), 766-779.


Cite as: https://hdl.handle.net/11858/00-001M-0000-0010-8886-1
Abstract
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide 13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome. [Supplemental material is available online at www.genome.org.]