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.

Latest release: FPC V9.1 (3 Jul 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 V9.1 release (July 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:

• Hosted by AGI/AGCOL: Rice Maize, Sorghum
• Hosted at AGCoL, created at TAIR/GSC Arabidopsis thaliana
• Hosted at AGCoL, created at GSC Human
• Sanger Center Zebrafish, Porcine
• Kango Kangaroo
• BBSRC Brassica rapa A, Brassica oleracea C
  
• LiveStock Genomics Cattle

• 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).

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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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