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Related Experiment Videos

ESTree db: a tool for peach functional genomics.

Barbara Lazzari1, Andrea Caprera, Alberto Vecchietti

  • 1Parco Tecnologico Padano, Via Einstein, Località Cascina Codazza, 26900 Lodi, Italy. barbara.lazzari@tecnoparco.org

BMC Bioinformatics
|December 15, 2005
PubMed
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The ESTree database provides a comprehensive resource for peach functional genomics, integrating over 18,000 expressed sequence tags (ESTs) with valuable annotation and search functionalities.

Area of Science:

  • Plant genomics
  • Functional genomics
  • Bioinformatics

Background:

  • The ESTree database aggregates Prunus persica expressed sequence tags (ESTs) for peach functional genomics.
  • It includes 6,155 in-house EST sequences and 12,475 from public databases.

Purpose of the Study:

  • To create a centralized, searchable database of peach ESTs.
  • To facilitate research in peach functional genomics.

Main Methods:

  • Developed an automated pipeline using Perl scripts and public software for EST processing.
  • Collected data in a MySQL database with a PHP web interface.
  • Performed contig assembly using CAP3 and SNP detection with AutoSNP.

Main Results:

Related Experiment Videos

  • The ESTree db (April 2005) contains 18,630 sequences from eight libraries.
  • Sequences were annotated using BLASTx and Gene Ontology (GOblet).
  • Provided links to NiceZyme and KEGG pathways, with local BLAST and text search utilities.

    • Conclusions:

    • The ESTree db is a comprehensive resource for peach EST data and related links.
    • Sequence and Contig Report pages offer quick access to detailed information.