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JESAM: CORBA software components to create and publish EST alignments and clusters.

J D Parsons1, P Rodriguez-Tomé

  • 1EMBL-Outstation, The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. jparsons@ebi.ac.uk

Bioinformatics (Oxford, England)
|June 27, 2000
PubMed
Summary

This study introduces JESAM software for creating customized Expressed Sequence Tag (EST) databases, improving data accessibility and reducing redundancy. The software offers a better approach to analyzing EST data for research.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Expressed Sequence Tags (ESTs) are valuable for gene discovery but suffer from high redundancy and errors in public databases.
  • Existing EST databases lack transparency in their derivation, hindering trust, correction, and customization.
  • Previous approaches often involve redundant work due to difficulties in accessing and reusing intermediary results.

Purpose of the Study:

  • To present the JESAM software as a solution for creating customized EST-derived databases.
  • To address the limitations of existing EST databases by providing accessible intermediary results.
  • To facilitate efficient and customized analysis of EST data for various research applications.

Main Methods:

  • Self-comparison of EST and full-length mRNA sequences for four model organisms using overlap analysis.

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  • Parallel sequence comparisons via a PVM process farm for efficient computation.
  • Publication of overlap databases with CORBA interfaces for flexible global access.

    • Main Results:

    • Developed and published overlap databases for EST and mRNA sequences with CORBA interfaces.
    • Created simple cDNA supercluster databases accessible via CORBA interfaces and browsable with applets.
    • Demonstrated advantages over existing databases like UniGene Mouse and Rat by offering contrasting perspectives on complex data.

    Conclusions:

    • JESAM software enables efficient creation of customized EST databases through accessible intermediary results.
    • The CORBA interfaces provide flexible global access to analyzed EST data.
    • This approach overcomes limitations of existing databases, promoting more effective research.