Plant Physiology 138:116-126 (2005)
© 2005 American Society of Plant Biologists
BIOINFORMATICS
FPC Web Tools for Rice, Maize, and Distribution1
Vishal Pampanwar,
Friedrich Engler,
James Hatfield,
Steve Blundy,
Gaurav Gupta and
Carol Soderlund*
Arizona Genomic Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, Arizona 85721 (V.P., F.E., J.H., G.G., C.S.); and Clemson University, Clemson, South Carolina 29634 (S.B.)
Many clone-based physical maps have been built with the FingerPrinted Contig (FPC) software, which is written in C and runs locally for fast and flexible analysis. If the maps were viewable only from FPC, they would not be as useful to the whole community since FPC must be installed on the user machine and the database downloaded. Hence, we have created a set of Web tools so users can easily view the FPC data and perform salient queries with standard browsers. This set includes the following four programs: WebFPC, a view of the contigs; WebChrom, the location of the contigs and genetic markers along the chromosome; WebBSS, locating user-supplied sequence on the map; and WebFCmp, comparing fingerprints. For additional FPC support, we have developed an FPC module for BioPerl and an FPC browser using the Generic Model Organism Project (GMOD) genome browser (GBrowse), where the FPC BioPerl module generates the data files for input into GBrowse. This provides an alternative to the WebChrom/WebFPC view. These tools are available to download along with documentation. The tools have been implemented for both the rice (Oryza sativa) and maize (Zea mays) FPC maps, which both contain the locations of clones, markers, genetic markers, and sequenced clone (along with links to sites that contain additional information).
1 This work was supported in part by the U.S. Department of Agriculture Initiative for Future Agriculture and Food Systems (grant no. 11180) and by the National Science Foundation (grant no. 0213764).
www.plantphysiol.org/cgi/doi/10.1104/pp.104.056291.
* Corresponding author; e-mail cari{at}agcol.arizona.edu; fax 5206262632.
Received November 18, 2004;
returned for revision February 15, 2005;
accepted February 20, 2005.
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