FPC

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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.

Page Contents:

FPC downloads, tutorials, and documentation

References

Other relevant links:

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

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

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References

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

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

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

Book chapters

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

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

Other

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

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.

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

Email Comments To: fpc@agcol.arizona.edu