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Related Experiment Videos

GBuilder--an application for the visualization and integration of EST cluster data.

J Muilu1, P Rodriguez-Tomé, A Robinson

  • 1European Bioinformatics Institute, European Molecular Biology Laboratory Outstation-Hinxton, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. muili@ebi.ac.uk

Genome Research
|January 13, 2001
PubMed
Summary

GBuilder is a Java tool for visualizing and analyzing DNA sequences, especially challenging EST data. It integrates diverse online data sources and analysis applications for comprehensive sequence exploration.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Analyzing large-scale DNA sequence data, particularly Expressed Sequence Tags (ESTs), presents significant challenges due to redundancy and data quality issues.
  • Existing tools often lack integrated functionality for diverse data sources and analysis applications, hindering comprehensive exploration.
  • Effective visualization and analysis are crucial for understanding sequence clusters and assemblies.

Purpose of the Study:

  • To introduce GBuilder, a network-centric DNA sequence visualization and analysis tool.
  • To provide an easy-to-use Java application for analyzing DNA sequence clusters and assemblies, with a focus on EST data.
  • To enable integration of external data sources and analysis applications for enhanced functionality.

Main Methods:

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  • Development of a Java-based application for DNA sequence visualization and analysis.
  • Implementation of network-centric capabilities for accessing and integrating diverse online data.
  • Utilizing Common Object Request Broker Architecture (CORBA) for seamless integration of external resources and applications.
  • Support for visualization at nucleotide and annotation levels, with manual sequence editing.

Main Results:

  • GBuilder offers versatile visualization of sequence similarities and dissimilarities.
  • The tool successfully integrates external EST cluster databases and command-line analysis applications via CORBA.
  • Manual sequence editing is supported, enhancing analytical flexibility.
  • Facilitates exploration of complex and redundant EST datasets.

Conclusions:

  • GBuilder provides a powerful and flexible platform for DNA sequence analysis, particularly for EST data.
  • Its network-centric design and integration capabilities streamline the analysis workflow.
  • The tool enhances the ability to explore and understand complex genomic datasets.