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



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ID: 229726.0, 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, Claudia; Bosdet, Ian; Chiu, Readman; Graves, Tina; Hummel, Oliver; Layman, Dan; Mathewson, Carrie; 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; Tänzer, 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, Steven; Marra, Marco; Schein, Jacqueline
Language:English
Date of Publication (YYYY-MM-DD):2004-04-01
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:Experts Only
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.
Comment of the Author/Creator:[Supplemental material is available online at www.genome.org.]
External Publication Status:published
Document Type:Article
Version Comment:Automatic journal name synchronization
Communicated by:Hans Lehrach
Affiliations:MPI für molekulare Genetik
External Affiliations:Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada V5Z 4E6;
Genome Sequencing Centre, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
Max-Delbruck-Center for Molecular Medicine (MDC), 13125 Berlin-Buch, Germany;
BACPAC Resources, Children's Hospital Oakland Research Institute, Oakland, California 94609, USA;
Department of Physics and Astronomy, University of British Columbia, Vancouver, Canada V6T 1Z1;
Department of Genome Analysis, Institute of Molecular Biotechnology, 07745 Jena, Germany;
The Institute for Genomic Research, Rockville, Maryland 20850, USA.
Identifiers:ISSN:1088-9051
DOI:10.1101/gr.2336604.
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