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The Diatom EST Database.

Uma Maheswari1, Anton Montsant, Johannes Goll

  • 1Avestha Gengraine Technologies Pvt. Ltd, Discoverer, 9th Floor, International Technology Park, Whitefield Road, Bangalore 560066, India.

Nucleic Acids Research
|December 21, 2004
PubMed
Summary
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The Diatom EST database offers access to expressed sequence tag (EST) data for Phaeodactylum tricornutum and Thalassiosira pseudonana. This resource facilitates research on microalgae by providing annotated ESTs and facilitating data retrieval.

Area of Science:

  • Marine biology
  • Bioinformatics
  • Algal genomics

Background:

  • Expressed Sequence Tags (ESTs) are crucial for understanding gene expression in organisms.
  • Diatoms, like Phaeodactylum tricornutum and Thalassiosira pseudonana, are ecologically significant microalgae with complex genomes.
  • Integrated databases are needed to manage and analyze large-scale EST data.

Purpose of the Study:

  • To create a centralized, integrated database for diatom EST data.
  • To provide comprehensive access to annotated EST sequences for P. tricornutum and T. pseudonana.
  • To facilitate comparative genomics and functional studies in diatoms.

Main Methods:

  • Clustering and assembly of approximately 30,000 EST sequences for each organism.
  • Automated annotation of non-redundant ESTs using protein and domain similarity searches.

Related Experiment Videos

  • Development of a relational database management system (RDBMS) with a user-friendly web interface.

    • Main Results:

    • The Diatom EST database (PtDB and TpDB) contains non-redundant, assembled ESTs for P. tricornutum and T. pseudonana.
    • Automated annotation includes similarity searches against protein databases, Pfam domains, COGs, and GOs.
    • A codon usage table derived from the EST data is also available.

    Conclusions:

    • The Diatom EST database provides a valuable, accessible resource for diatom research.
    • The integrated data and user-friendly interface support keyword, BLAST, and functional domain-based searches.
    • This database will aid in advancing the study of diatom biology and genomics.