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This work was funded in part by the Initiative for Future Agriculture and Food Systems Grant no. 2001-52100-11292 from the USDA Cooperative State Research, Education, and Extension Service.

Bioperl module for FPC: This module is part of the latest (1.5.1) release of bioperl. The FPC bioperl module reads an FPC file and allows different queries including the computation of the Sulston score. The Module Documentation is in the format used by bioperl and lists all queries.

FPC Genome Browser: The GMOD Genome Browser (Gbrowse) uses a configuration file and a mySQL database. We provide the configuration file for FPC along with the script to translate an FPC file into the GFF format into the mySQL database; the script uses the FPC bioperl module. The configuration and gff file works with the GMOD CGI interface or the AGCoL Java Gbrowse interface.

Bioperl module for FPC
Module Documentation
Recent updates
Simple Testcase
Advanced Testcases
FPC Genome Browser
  Configuration File
  GFF File and Script
  Demo of sample files with Java Gbrowse

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References

Pampanwar, V., F. Engler, J. Hatfield, S. Blundy, G. Gupta, and C. Soderlund (2005). FPC web tools for maize, rice, and distribution. Plant Physiology, in press.

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

Stajich,J., D.Block, K.Boulez, S.Brenner, S.Chervitz, C.Dagdigian, G.Fuellen, J.Gilbert, I.Korf, H.Lapp, H.Lehvaslaiho, C.Matsalla, C.Mungall, B.Osborne, M.Pocock, P.Schattner, M.Senger, L.Stein, E.Stupka, M.Wilkinson, and E.Birney (2002) The Bioperl Toolkit: Perl Modules for the Life Sciencesr. Genome Research 10:1611-1618.

Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., and Lewis, S. (2002) The generic genome browser: a building block for a model organism system database. Genome Research 12:1599-610.


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