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

Latest release: FPC V9 (28 Feb 2008);
Publication of paper on HICF in Plant Physiology, see references

Contents:
FPC downloads, tutorials, and documentation
Web-based FPC Maps
References
Other relevant links:
  WebAGCoL - web based FPC tools
  BioFPC - FPC for bioPerl and Gbrowse
  Simulations - Methods, Error and MTP simulations
  SyMAP - Compare a FPC map against a genomic sequence

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FPC downloads, tutorials and documentation

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.

FPC V9 release (Feb 2008, details) 

Download Documentation Description
FPC Documentation Guide FPC tar file, executables, and user's guide
demo.tar FPC Tutorial* (.doc) Tutorial of salient features
ctgdemo.tar Contig display tutorial Tutorial on new contig display features
bssdemoV2.tar.gz BSS tutorial Tutorial on BSS (runs BLAST/BLAT and adds results to FPC)
NEW seqdemo.tar.gz Sequence track tutorial Tutorial on using the FPC draft sequence alignment functions
mtpdemoV2.tar MTP tutorial Tutorial on automatically select minimal tiling path in FPC
hicf_auto.tar HICF & Auto Merge tutorial Tutorial on assembling HICF and performing auto merging
fsd.tar FSD and FSD2 Manual Program to extract Sequence and FPC Simulated Digest

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

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Web-based FPC Maps

A Web based Java program displays the contigs for the following FPC databases:

Also see:
  • GSC: human, mouse, Arabidopsis thaliana, Salmonella enterica.
  • BCGSC: human, mouse, rat, bovine, C.neoformans.
  • Sanger: mouse-human synteny.
  • TAMU: soybean, arabidopsis, chicken, indica rice.
  • UCDavis: wheat, potato.
  • Gramene: map viewer for comparative mapping (Maps Viewer).
  • NCBI: mouse map (see Maps&Options).
Let us know if you would like us to set up your FPC file as a WebFPC. For example, we have recently done this for TAIR. Once installed, we can continue to host it, or turn it over to the host lab.

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References

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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Email Comments To: fpc@agcol.arizona.edu