The University of Arizona
FPC (FingerPrinted Contigs)  
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This work was funded in part by NSF grant #0213764 and by the Initiative for Future Agriculture and Food Systems Grant no. 2001-52100-11292 from the USDA Cooperative State Research, Education, and Extension Service.

FPC takes as input a set of clones and their restriction fragments (called Bands) and assembles the clones into contigs; for more information, see summary. FPC contributions are by the GSC, BCGSC, Sanger Centre, Clemson University, and University of Arizona.

Latest release: FPC V9.4 (21 Mar 2011) support for sequence based fingerprints (see details)

Page Contents:
FPC downloads, tutorials, and documentation
References
Other relevant links:
  WebAGCoL - web based FPC tools
  SyMAP - Compare a FPC map against a genomic sequence

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FPC downloads, tutorials and documentation

FPC binaries, tutorials, documentation, and source code have been collected into a single download package.
View the Readme.

The FPC Package contains the following (linked documents are viewable online):

Item Description
FPC V9.4 binaries binaries are provided for 32 and 64 bit Linux, and Windows
FPChelpdoc.htm Provides the interactive help accessible from FPC
FPC Tutorial* Introductory tutorial and demo of core features
Contig display tutorial Tutorial on new contig display features
BSS tutorial Tutorial on BSS (runs BLAST/BLAT and adds results to FPC)
Sequence track tutorial Tutorial on using the FPC draft sequence alignment functions
MTP tutorial Tutorial on automatically select minimal tiling path in FPC
HICF & Auto Merge tutorial Tutorial on assembling HICF and performing auto merging
FSD and FSD2 Programs to perform in-silico agarose fingerprinting
fpc_source.tar FPC source code
fpcV8.5.3.OSX V8.5.3 Mac binary
fpcV8.5.3.SUN V8.5.3 Solaris binary

*Published in Ian Dunham (ed) Genomic Mapping and Sequencing, Horizon Press, Genome Technology series.

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References

van Oeveren J, de Ruiter M, Jesse T, van der Poel H, Tang J, Yalcin F, Janssen A, Volpin H, Stormo KE, Bogden R, van Eijk MJ, Prins M (2011). Sequence-based physical mapping of complex genomes by whole genome profiling. Genome Res., epub Feb. 1, 2011. Download

Nelson, W. and C. Soderlund (2009). Integrating Sequence with FPC Fingerprinted Maps. Nucleic Acids Research 1-11 doi:10.1093/nar/gkp034 Download

Nelson, W., J. Dvorak, M. Luo, J. Messing, R. Wing, and C. Soderlund (2006). Efficacy of clone fingerprinting methodologies. Genomics 89:160-165. Download

Nelson, W, A Bharti, E Butler, F Wei, G Fuks, H Kim, R Wing, J Messing, and C Soderlund (2005). Whole-Genome Validation of High-Information-Content Fingerprinting. Plant Physiology 139:27-38. Download

Nelson, W. and C. Soderlund (2005). Software for restriction fragment physical maps. K. Meksem, G. Kahl (ed) The Handbook of Genome Mapping: Genetic and Physical Mapping, Wiley-VCH. pp. 285-306. Download

Engler, F., J. Hatfield, W. Nelson, and C. Soderlund (2003). Locating sequence on FPC maps and selecting a minimal tiling path. Genome Research 13:2152:2163. Download   Supplemental

Engler, F. and C. Soderlund (2002). Software for Physical Maps. In Ian Dunham (ed) Genomic Mapping and Sequencing, Horizon Press, Genome Technology series. Norfolk, UK, pp. 201-236.

Soderlund, C., F. Engler, J. Hatfield, S. Blundy, M. Chen, Y. Yu, and R. Wing (2002). Mapping sequence to Rice FPC. In P. Wang, J. Wang and C. Wu (ed) Computational Biology and Genome Informatics. World Scientific Publishing. pp 59-79. Download.

Ness, S.R., Terpstra, W., Krzywinski, M., Marra M., Jones, A., and Ness, S.J.M. (2002). Assembly of fingerprint contigs: parallelized FPC. BioInformatics 18:484-485.

Chen, M., Presting, G., Barbazuk, W., Goicoechea, J., Blackmon, B., Fang, G., Kim, H., Frisch, D., Yu, Y., Higingbottom, S., Phimphilai, J., Phimphilai, D., Thurmond, S., Gaudette, B., Li, P., Liu, J., Hatfield, J., Sun, S., Farrar, K., Henderson, C., Barnett, L., Costa, R., Williams, B., Walser, S., Atkins, M., Hall, C., Bancroft, I., Salse, J., Regad, F., Mohapatra, T., Singh, N., Tyagi, A., Soderlund, C., Dean, R., and Wing, R. (2002). An integrated physical and genetic map of the rice genome. Plant Cell.

The International Human Genome Mapping Consortium (2001) A physical map of the human genome, Nature 409:934-941 Download.

Soderlund, C., S. Humphrey, A. Dunhum, and L. French (2000). Contigs built with fingerprints, markers and FPC V4.7. Genome Research 10:1772-1787. Download.

Soderlund, C., S. Gregory and I. Dunham (1998). Sequence ready clones. In Bishop, M.J. (ed) Guide to Human Genome Computing, Academic Press.

Mungal, A., S. Humphray, S. Ranby, C. Edwards, R. Heathcott, C. Clee, E. Holloway, A. Peck, P. Harrision, L. Green, A. Butler, C. Langford, R. Gwilliam, E. Huckle, L. Baron, A. Smith, M. Leversha, Y. Ramsey, S. Clegg, C. Rice, G. Maslen, S. Hunt, C. Scott, S. Soderlund, A. Theaker, N. Carter, M. Ross, P. Deloukas, D. Bentley, I. Dunham (1997) From Long Range Mapping to Sequence Ready Contigs on Human Chromosome 6. DNA sequence - The Journal of Sequencing and Mapping, 8:151-154.

Soderlund, C., I. Longden and R. Mott (1997) FPC: a system for building contigs from restriction fingerprinted clones. CABIOS, 13: 523-535. Download.

Gregory, S., C. Soderlund and A. Coulson (1996) Contig assembly by fingerprinting. In P. H. Dear (ed) Genome Mapping: a Practical Approach.

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Last Modified Tuesday October 09, 2012 16:37 PM and 54 seconds