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Related Experiment Videos

ESTuber db: an online database for Tuber borchii EST sequences.

Barbara Lazzari1, Andrea Caprera, Cristian Cosentino

  • 1Istituto di Biologia e Biotecnologia Agraria, via Bassini 15, 20133 Milan, Italy. lazzari@ibba.cnr.it

BMC Bioinformatics
|April 14, 2007
PubMed
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The ESTuber database provides a valuable resource for studying truffle genes, housing over 3,000 expressed sequence tags (ESTs) from Tuber borchii. This curated database facilitates research into truffle gene expression and function.

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • The ESTuber database contains 3,271 Tuber borchii expressed sequence tags (ESTs).
  • Data includes 2,389 sequences from truffle vegetative hyphae and 882 from GenBank, covering various developmental stages.
  • An automated pipeline processed EST sequences using public and custom Perl scripts.

Purpose of the Study:

  • To create a comprehensive, queryable database of Tuber borchii expressed sequence tags.
  • To facilitate research on truffle gene expression and function.
  • To provide a web-accessible resource for truffle genomics data.

Main Methods:

  • EST sequences were clustered and annotated against GenBank nr, UniProtKB, and a fungi genomic database.
  • An algorithm inferred Gene Ontology (GO) categories from UniProtKB annotations.

Related Experiment Videos

  • Analyses included tandem repeats search and protein pattern identification against PROSITE.

    • Main Results:

    • The ESTuber database integrates 3,271 Tuber borchii ESTs.
    • Annotation against multiple databases provided functional insights.
    • Comparative analyses were performed on complete and assembled EST sequences.

    Conclusions:

    • The ESTuber website serves as a data and link repository for truffle expressed genes.
    • Sequence and Contig Report pages offer core web interface functionalities.
    • Text search and BLAST utilities enable easy data access.