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Methods: SyMAP: A system for discovering and viewing syntenic regions of FPC maps
- Carol Soderlund,
- William Nelson,
- Austin Shoemaker,
- and Andrew Paterson
Genome Res. September 2006 16: 1159-1168; doi:10.1101/gr.5396706
...developed a system to align an FPC-based physical map to a genomic sequence based on BAC end sequences and sequence-tagged hybridization markers and to align two FPC maps to one another based on shared markers and fingerprints. The system, called SyMAP (Synteny Mapping and Analysis Program), consists...
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Methods: Locating Sequence on FPC Maps and Selecting a Minimal Tiling Path
- Friedrich W. Engler,
- James Hatfield,
- William Nelson,
- and Carol A. Soderlund
Genome Res. September 2003 13: 2152-2163; Published in Advance January 1, 2003, doi:10.1101/gr.1068603
...at once. The third tool, pickMTP, automates the majority of this last usage of BSS. Results are presented using the rice FPC map, BAC end sequences, and whole- shotgun from Syngenta. FPC (FingerPrinted Contigs; Soderlund et al. 1997 ) maps are built from fingerprinted clones and annotated with markers...
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RESOURCE: A BAC-based physical map of the Drosophila buzzatii genome
- Josefa González,
- Michael Nefedov,
- Ian Bosdet,
- Ferran Casals,
- Oriol Calvete,
- Alejandra Delprat,
- Heesun Shin,
- Readman Chiu,
- Carrie Mathewson,
- Natasja Wye,
- Roger A. Hoskins,
- Jacqueline E. Schein,
- Pieter de Jong,
- and Alfredo Ruiz
Genome Res. June 2005 15: 885-892; doi:10.1101/gr.3263105
...., Longden, I., and Mott, R. 1997 . FPC: A system for building contigs from restriction fingerprinted clones. Comput. Appl. Biosci. 13 : 523 -535. ↵ Soderlund, C., Humphray, S., Dunham, A., and French, L. 2000 . Contigs built with fingerprints, markers, and FPC V4.7. Genome Res. 10 : 1772 -1787. ↵ Spencer, W...
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Methods: Physical map-assisted whole-genome shotgun sequence assemblies
- René L. Warren,
- Dmitry Varabei,
- Darren Platt,
- Xiaoqiu Huang,
- David Messina,
- Shiaw-Pyng Yang,
- James W. Kronstad,
- Martin Krzywinski,
- Wesley C. Warren,
- John W. Wallis,
- LaDeana W. Hillier,
- Asif T. Chinwalla,
- Jacqueline E. Schein,
- Asim S. Siddiqui,
- Marco A. Marra,
- Richard K. Wilson,
- and Steven J.M. Jones
Genome Res. June 2006 16: 768-775; doi:10.1101/gr.5090606
...: Parallelized FPC. Bioinformatics 18 : 484 – 485 . ↵ Soderlund C. , Longden I. , Mott R. ( 1997 ) FPC: A system for building contigs from restriction fingerprinted clones. Comput. Appl. Biosci. 13 : 523 – 535 . ↵ Soderlund C. , Humphray S. , Dunham A. , French L. ( 2000 ) Contigs built with fingerprints...
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Methods: Fosmid-Based Physical Mapping of the Histoplasma capsulatum Genome
- Vincent Magrini,
- Wesley C. Warren,
- John Wallis,
- William E. Goldman,
- Jian Xu,
- Elaine R. Mardis,
- and John D. McPherson
Genome Res. August 2004 14: 1603-1609; doi:10.1101/gr.2361404
...: 1368 –1372. ↵ Soderlund, C., Humphray, S., Dunham, A., and French, L. 2000 . Contigs built with fingerprints, markers, and FPC V4.7. Genome Res. 10 : 1772 –1787. ↵ Sorensen, K.N., Clemons, K.V., and Stevens, D.A. 1999 . Murine models of blastomycosis, coccidioidomycosis, and histoplasmosis...
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RESOURCE: A Marker-Dense Physical Map of the Bradyrhizobium japonicum Genome
- Jeffrey P. Tomkins,
- Todd C. Wood,
- Minviluz G. Stacey,
- John T. Loh,
- Adam Judd,
- Jose L. Goicoechea,
- Gary Stacey,
- Michael J. Sadowsky,
- and Rod A. Wing
Genome Res. August 1, 2001 11: 1434-1440; doi:10.1101/gr.185001
....S. , Baptista C.S. , et al. ( 2000 ) The sequence of the plant pathogen Xylella fastidiosa. Nature 406 : 151 – 159 . ↵ Soderlund C. , Humphray S. , Dunham A. , French L. ( 2000 ) Contigs built with fingerprints, markers, and FPC v4.7. Genome Res. 20 : 1772 – 1787 . ↵ Tomkins J.P. , Miller-Smith H. , Sasinowski...
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LETTER: A 12-Mb Complete Coverage BAC Contig Map in Human Chromosome 16p13.1–p11.2
- Yicheng Cao,
- Hyung Lyun Kang,
- Xuequn Xu,
- Mei Wang,
- So Hee Dho,
- Jun Ryul Huh,
- Byeong-Jae Lee,
- Francis Kalush,
- Diana Bocskai,
- Yan Ding,
- Judith G. Tesmer,
- Jonghyeob Lee,
- Eunpyo Moon,
- Vesna Jurecic,
- Antonio Baldini,
- Heinz-Ulrich Weier,
- Norman A. Doggett,
- Melvin I. Simon,
- Mark D. Adams,
- and Ung-Jin Kim
Genome Res. August 1, 1999 9: 763-774; doi:10.1101/gr.9.8.763
...—corresponding to a total of 7.721 Mb of genomic DNA—have been sequenced, and provides a high resolution physical map of the region. Contigs were initially built based mainly on the analysis of STS contents and restriction fingerprint patterns of the clones. To close the gaps, probes derived from BAC clone ends were used...
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RESOURCE: Internet Contig Explorer (iCE)—A Tool for Visualizing Clone Fingerprint Maps
- Christopher D. Fjell,
- Ian Bosdet,
- Jacqueline E. Schein,
- Steven J.M. Jones,
- and Marco A. Marra
Genome Res. June 2003 13: 1244-1249; doi:10.1101/gr.819303
.... CABIOS 13 : 523 –535. ↵ Soderlund, C., Humphray, S., Dunham, I. and French, L. 2000 . Contigs built with fingerprints, markers, and FPC V4.7. Genome Res. 11 : 934 –941. ↵ Sulston, J., Mallett, F., Staden, R., Durbin, R., Horsnell, T., and Coulson, A. 1988 . Software for mapping by fingerprinting...
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RESOURCE: A BAC-Based Physical Map of the Chicken Genome
- Chengwei Ren,
- Mi-Kyung Lee,
- Bo Yan,
- Kejiao Ding,
- Bettye Cox,
- Michael N. Romanov,
- Jennifer A. Price,
- Jerry B. Dodgson,
- and Hong-Bin Zhang
Genome Res. December 2003 13: 2754-2758; doi:10.1101/gr.1499303
.... Cytogenet. Cell Genet. 90 : 169 -218. ↵ Soderlund, C., Longden, I., and Mott, R. 1997 . FPC: A system for building contigs from restriction fingerprinted clones. CABIOS 13 : 523 -535. ↵ Soderlund, C., Humphray, S., Dunham, A., and French, L. 2000 . Contigs built with fingerprints, markers, and FPC V4...
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RESOURCE: A BAC- and BIBAC-Based Physical Map of the Soybean Genome
- Chengcang Wu,
- Shuku Sun,
- Padmavathi Nimmakayala,
- Felipe A. Santos,
- Khalid Meksem,
- Rachael Springman,
- Kejiao Ding,
- David A. Lightfoot,
- and Hong-Bin Zhang
Genome Res. February 2004 14: 319-326; Published in Advance January 12, 2004, doi:10.1101/gr.1405004
..., C., Humphray, S., Dunham, A., and French, L. 2000 . Contigs built with fingerprints, markers, and FPC V4.7. Genome Res. 10 : 1772 -1787. ↵ Spring, J. 1997 . Vertebrate evolution by interspecific hybridization: Are we polyploid? FEBS Lett. 400 : 2 -8. ↵ Sulston, J., Mallett, F., Staden, R., Durbin, R...

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