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RESOURCE: Physical Maps for Genome Analysis of Serotype A and D Strains of the Fungal Pathogen Cryptococcus neoformans
- Jacqueline E. Schein,
- Kristin L. Tangen,
- Readman Chiu,
- Heesun Shin,
- Klaus B. Lengeler,
- William Kim MacDonald,
- Ian Bosdet,
- Joseph Heitman,
- Steven J.M. Jones,
- Marco A. Marra,
- and James W. Kronstad
Genome Res. September 1, 2002 12: 1445-1453; Published in Advance August 21, 2002, doi:10.1101/gr.81002
...where the joins did not result in inconsistencies in the fingerprint data. Upon completion of these manual edits, the JEC21 map contained 2322 clones, the H99 map contained 2529 clones, and each map had been assembled into 20 sequence-ready contigs. An example of the FPC display for the contig...
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LETTER: A High-throughput AFLP-based Method for Constructing Integrated Genetic and Physical Maps: Progress Toward a Sorghum Genome Map
- Patricia E. Klein,
- Robert R. Klein,
- Samuel W. Cartinhour,
- Paul E. Ulanch,
- Jianmin Dong,
- Jacque A. Obert,
- Daryl T. Morishige,
- Shannon D. Schlueter,
- Kevin L. Childs,
- Melissa Ale,
- and John E. Mullet
Genome Res. June 1, 2000 10: 789-807; doi:10.1101/gr.10.6.789
...for the presence of multiple clones containing the same PCR product. The DNA pooling strategy was also designed for use with multiplexed PCR assays that would allow parallel identification of numerous BAC contigs; each containing a different PCR-amplified marker. The pooling strategy implemented here consisted...
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LETTER: Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
- Ge Liu,
- NISC Comparative Sequencing Program,
- Shaying Zhao,
- Jeffrey A. Bailey,
- S. Cenk Sahinalp,
- Can Alkan,
- Eray Tuzun,
- Eric D. Green,
- and Evan E. Eichler
Genome Res. March 1, 2003 13: 358-368; doi:10.1101/gr.923303
....D. , Itoh T. , Tsai S.F. , Park H.S. , Yaspo M.L. , Lehrach H. , Chen Z. , et al. ( 2002 ) Construction and analysis of a human-chimpanzee comparative clone map. Science 295 : 131 – 134 . ↵ Gilbert N. , Lutz-Prigge S. , Moran J.V. ( 2002 ) Genomic deletions created upon LINE-1 retrotransposition. Cell 110...
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LETTER: Pericentromeric Duplications in the Laboratory Mouse
- James W. Thomas,
- Mary G. Schueler,
- Tyrone J. Summers,
- Robert W. Blakesley,
- Jennifer C. McDowell,
- Pamela J. Thomas,
- Jacquelyn R. Idol,
- Valerie V.B. Maduro,
- Shih-Queen Lee-Lin,
- Jeffrey W. Touchman,
- Gerard G. Bouffard,
- Stephen M. Beckstrom-Sternberg,
- NISC Comparative Sequencing Program,
- and Eric D. Green
Genome Res. January 1, 2003 13: 55-63; Published in Advance December 30, 2002, doi:10.1101/gr.791403
.... ↵ Thomas J.W. , Prasad A.B. , Summers T.J. , Lee-Lin S.-Q. , Maduro V.V.B. , Idol J.R. , Ryan J.F. , Thomas P.J. , McDowell J.C. , Green E.D. ( 2002 ) Parallel construction of orthologous sequence-ready clone contig maps in multiple species. Genome Res. 12 : 1277 – 1285 . ↵ Venter J.C. , Adams M.D. , Myers...
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Chicken Special/Resources: Uprobe: A genome-wide universal probe resource for comparative physical mapping in vertebrates
- Wendy A. Kellner,
- Robert T. Sullivan,
- Brian H. Carlson,
- and James W. Thomas
Genome Res. January 2005 15: 166-173; Published in Advance December 8, 2004, doi:10.1101/gr.3066805
...set of detailed protocols for use of the universal probes can be obtained from http://uprobe.genetics.emory.edu/process.php . Quantification of universal probe specificity The combination of BAC clone probe-content maps and restriction-enzyme fingerprint contigs was used to assess whether or not each...
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RESOURCE: A Cattle–Human Comparative Map Built with Cattle BAC-Ends and Human Genome Sequence
- Denis M. Larkin,
- Annelie Everts-van der Wind,
- Mark Rebeiz,
- Peter A. Schweitzer,
- Sharon Bachman,
- Cheryl Green,
- Chris L. Wright,
- Edhilvia J. Campos,
- Leslie D. Benson,
- Jennifer Edwards,
- Lei Liu,
- Kazutoyo Osoegawa,
- James E. Womack,
- Pieter J. de Jong,
- and Harris A. Lewin
Genome Res. August 2003 13: 1966-1972; doi:10.1101/gr.1560203
...genomics. Trends Genet. 18 : 104 -108. ↵ Thomas, J.W., Prasad, A.B., Summers, T.J., Lee-Lin, S.Q., Maduro, V.V., Idol, J.R., Ryan, J.F., Thomas, P.J., McDowell, J.C., and Green, E.D. 2002 . Parallel construction of orthologous sequence-ready clone contig maps in multiple species. Genome Res. 12 : 1277...
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LETTER: Close Split of Sorghum and Maize Genome Progenitors
- Zuzana Swigoňová,
- Jinsheng Lai,
- Jianxin Ma,
- Wusirika Ramakrishna,
- Victor Llaca,
- Jeffrey L. Bennetzen,
- and Joachim Messing
Genome Res. October 2004 14: 1916-1923; doi:10.1101/gr.2332504
.../2 . For each of the BAC contigs, their actual orientations in the chromosomes are not known. The Zmfie1 and Zmfie2 are not a strict orthologous pair (see explanation in text), thus, are not included in our sequence analysis. RESULTS Isolation of BAC Clones and Their Sequencing Probes for six loci ( c1/pl1, tbp...
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LETTER: Noncoding Sequences Conserved in a Limited Number of Mammals in the SIM2 Interval are Frequently Functional
- Kelly A. Frazer,
- Heng Tao,
- Kazutoyo Osoegawa,
- Pieter J. de Jong,
- Xiyin Chen,
- Mark F. Doherty,
- and David R. Cox
Genome Res. March 2004 14: 367-372; Published in Advance February 12, 2004, doi:10.1101/gr.1961204
....B., Summers, T.J., Lee-Lin, S.Q., Maduro, V.V., Idol, J.R., Ryan, J.F., Thomas, P.J., McDowell, J.C., and Green, E.D. 2002 . Parallel construction of orthologous sequence-ready clone contig maps in multiple species. Genome Res. 12 : 1277 –1285. ↵ Thomas, J.W., Touchman, J.W., Blakesley, R.W., Bouffard, G...
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LETTER: Comparative Genome Sequence Analysis of the Bpa/Str Region in Mouse and Man
- A.-M. Mallon,
- M. Platzer,
- R. Bate,
- G. Gloeckner,
- M.R.M. Botcherby,
- G. Nordsiek,
- M.A. Strivens,
- P. Kioschis,
- A. Dangel,
- D. Cunningham,
- R.N.A. Straw,
- P. Weston,
- M. Gilbert,
- S. Fernando,
- K. Goodall,
- G. Hunter,
- J.S. Greystrong,
- D. Clarke,
- C. Kimberley,
- M. Goerdes,
- K. Blechschmidt,
- A. Rump,
- B. Hinzmann,
- C.R. Mundy,
- W. Miller,
- A. Poustka,
- G.E. Herman,
- M. Rhodes,
- P. Denny,
- A. Rosenthal,
- and S.D.M. Brown
Genome Res. June 1, 2000 10: 758-775; doi:10.1101/gr.10.6.758
...in the sequence from clone 303O11. As would be expected from previous human mapping data, no F8A sequence was detectable in the corresponding human sequence contig. Zinc Finger Protein 275 A new zinc finger protein gene, Zfp275 , was identified distal of F8a in mouse contig B. A ZNF275 ortholog was also...
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LETTER: Comparative Genome Organization of Human, Murine, and Feline MHC Class II Region
- Naoya Yuhki,
- Thomas Beck,
- Robert M. Stephens,
- Yoko Nishigaki,
- Kymberly Newmann,
- and Stephen J. O'Brien
Genome Res. June 2003 13: 1169-1179; Published in Advance May 12, 2003, doi:10.1101/gr.976103
...). Briefly, this contig was generated by screening domestic cat PAC and BAC (RPCI 86) libraries using homologous MHC cDNA and PCR clones as probes. These DNA clones were then analyzed by restriction enzyme fingerprinting and assembled. Representative clones for a large-scale sequencing were selected in order...

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