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Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps.

Christopher D Fjell1, Ian Bosdet, Jacqueline E Schein

  • 1Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.

Genome Research
|June 12, 2003
PubMed
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A new Java application, iCE (Internet Contig Explorer), provides intuitive viewing of genomic fingerprint maps and data. This tool aids researchers in accessing and analyzing clone fingerprints and contig information for various species.

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Fingerprinted clone physical maps are essential for whole-genome sequencing, gene cloning, and comparative genomics.
  • Existing genomic databases require improved visualization tools for complex fingerprint data.

Purpose of the Study:

  • To introduce iCE (Internet Contig Explorer), a Java-based application for visualizing genomic fingerprint maps and associated data.
  • To provide researchers with an intuitive platform for exploring clone fingerprints, contigs, insert sizes, and markers.

Main Methods:

  • Development of a Java-based application, iCE (Internet Contig Explorer).
  • Implementation of features for searching and displaying individual clones, contigs, fingerprints, insert sizes, and markers.
  • Inclusion of functionality to load and view specific lists of clones and their fingerprints.

Related Experiment Videos

Main Results:

  • iCE facilitates the viewing of bacterial artificial chromosome (BAC) fingerprint maps for multiple species including mouse, rat, bovine, C. briggsae, and fungi.
  • The application is actively used in genome centers for managing and visualizing genomic data.
  • iCE supports the Rat Genome Sequencing Project by managing BAC clone provision for sequencing.

Conclusions:

  • iCE offers a valuable and intuitive tool for researchers working with genomic fingerprint maps.
  • The application enhances the accessibility and analysis of complex genomic data, supporting ongoing sequencing projects.