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          Institute: MPI für molekulare Genetik     Collection: Department of Vertebrate Genomics     Display Documents



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ID: 175369.0, MPI für molekulare Genetik / Department of Vertebrate Genomics
Integrated and sequence-ordered BAC and YAC-based physical maps for the rat genome
Authors:Krzywinski, Martin; Wallis, John; Goesele, Claaudia; Bosdet, Ian; Chiu, Readman; Graves, Tina; Hummel, Oliver; Layman, Dan; Mathewson, Carry; Wye, Natasja; Zhu, Baoli; Albracht, Derek; Asano, Jennifer; Barber, Sarah; Brown-John, Mabel; Chan, Susanna; Chand, Steve; Cloutier, Alison; Davito, Jonathon; Fjell, Chris; Gaige, Tony; Ganten, Detlev; Girn, Noreen; Guggenheimer, Kurtis; Himmelbauer, Heinz; Kreitler, Thomas; Leach, Stephen; Lee, Darlene; Lehrach, Hans; Mayo, Michael; Mead, Kelly; Olson, Teika; Pandoh, Pawan; Prabhu, Anna-Liisa; Shin, Heesun; Tanzer, Simone; Thompson, Jason; Tsai, Miranda; Walker, Jason; Yang, George; Sekhon, Mandeep; Hillier, LaDeana; Zimdahl, Heike; Marziali, Andre; Osoegawa, Kazutoyo; Zhao, Shaying; Siddiqui, Asim; de Jong, Pieter J.; Warren, Wes; Mardis, Elaine; McPherson, John D.; Wilson, Richard; Huebner, Norbert; Jones, Stephen; Marra, Marco; Schein, Jacqueline
Language:English
Date of Publication (YYYY-MM-DD):2004-04
Title of Journal:Genome Research
Journal Abbrev.:Genome Res.
Volume:14
Issue / Number:4
Start Page:766
End Page:779
Copyright:© 2004 by Cold Spring Harbor Laboratory Press.
Review Status:not specified
Audience:Not Specified
Abstract / Description: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.]
Comment of the Author/Creator:Date: 2004, APR
External Publication Status:published
Document Type:Article
Version Comment:Automatic journal name synchronization
Communicated by:Hans Lehrach
Affiliations:MPI für molekulare Genetik
External Affiliations:British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada.; Washington Univ, Sch Med, Genome Sequencing Ctr, St Louis, MO 63108 USA.; Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany.; Max Planck Inst Mol Genet, D-14195 Berlin, Germany.; Childrens Hosp Oakland, Res Inst, BACPAC Resources, Oakland, CA 94609 USA.; Univ British Columbia, Dept Phys & Astron, Vancouver, BC V6T 1Z1, Canada.; Inst Mol Biotechnol, Dept Genome Anal, D-07745 Jena, Germany.; Inst Genom Res, Rockville, MD 20850 USA.
Identifiers:ISI:000220629900032 [ID No:1]
ISSN:1088-9051 [ID No:2]
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