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Related Experiment Videos

FPC Web tools for rice, maize, and distribution.

Vishal Pampanwar1, Friedrich Engler, James Hatfield

  • 1Arizona Genomic Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA.

Plant Physiology
|May 13, 2005
PubMed
Summary

Web-based tools enhance access to FingerPrinted Contig (FPC) physical maps, enabling community-wide viewing and querying of FPC data without local software installation. These tools improve accessibility for rice and maize genome research.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • FingerPrinted Contig (FPC) software is crucial for building clone-based physical maps.
  • Local FPC installation and database downloads limit community-wide accessibility.

Purpose of the Study:

  • To develop web-based tools for accessible viewing and querying of FPC physical map data.
  • To enhance the utility of FPC maps for the broader scientific community.

Main Methods:

  • Developed a suite of four web tools: WebFPC, WebChrom, WebBSS, and WebFCmp.
  • Created an FPC module for BioPerl and integrated it with the Generic Model Organism Project (GMOD) genome browser (GBrowse).
  • Implemented tools for rice (Oryza sativa) and maize (Zea mays) FPC maps.

Main Results:

Related Experiment Videos

  • Web tools allow easy viewing of contigs, chromosome locations, and marker data via standard browsers.
  • BioPerl module and GBrowse integration provide an alternative visualization and data access method.
  • Tools facilitate locating clones, genetic markers, and sequenced clones with links to additional information.

Conclusions:

  • The developed web tools significantly improve accessibility and usability of FPC physical maps.
  • Enhanced data sharing and analysis capabilities for rice and maize genomics research.
  • These tools promote wider community engagement with FPC mapping data.