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PartiGene--constructing partial genomes.

John Parkinson1, Alasdair Anthony, James Wasmuth

  • 1School of Biological Sciences, Ashworth Laboratories, King's Buildings, West Mains Rd, University of Edinburgh, Edinburgh EH9 3JT, UK. jparkin@sickkids.ca

Bioinformatics (Oxford, England)
|February 28, 2004
PubMed
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PartiGene is a new bioinformatics tool that processes expressed sequence tags (ESTs) for gene discovery. It organizes genomic data, aids analysis, and creates accessible database resources for various organisms.

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Expressed sequence tags (ESTs) are crucial for gene discovery across diverse organisms.
  • Managing and analyzing large-scale EST data within a genomic context presents a significant challenge.

Purpose of the Study:

  • To introduce PartiGene, an integrated suite for processing and analyzing EST data.
  • To facilitate the organization of EST sequences within a genomic framework for large-scale analysis.
  • To enable customizable annotation and presentation of genomic data.

Main Methods:

  • Utilizes freely available public domain software for sequence processing.
  • Transforms raw trace chromatograms into sequence objects for dbEST submission.
  • Places sequences in a genomic context and performs first-pass annotation.

Related Experiment Videos

  • Presents data via HTML tables and an SQL database.

    • Main Results:

    • PartiGene successfully processes raw EST data into analyzable genomic information.
    • The suite enables the creation of non-model organism database resources like NEMBASE and LumbriBase.
    • The software is portable, free, and runs on standard Linux workstations.

    Conclusions:

    • PartiGene provides an effective solution for gene discovery and genomic data management.
    • The tool supports the development of valuable biological databases for research.
    • Its accessibility and portability make it suitable for various research laboratories.