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Related Experiment Videos

openSputnik--a database to ESTablish comparative plant genomics using unsaturated sequence collections.

Stephen Rudd1

  • 1Centre for Biotechnology, Tykistökatu 6, FIN-20521 Turku, Finland. stephen.rudd@btk.utu.fi

Nucleic Acids Research
|December 21, 2004
PubMed
Summary

Publicly available expressed sequence tag (EST) collections offer insights into plant genome evolution. The openSputnik database, with over a million unigenes from 50 species, aids in identifying lineage-specific genes and understanding plant evolution.

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Area of Science:

  • Plant genomics
  • Bioinformatics
  • Evolutionary biology

Background:

  • Public expressed sequence tag (EST) collections are expanding with diverse plant species data.
  • EST data, though biased, offers comparative insights into plant gene populations.

Purpose of the Study:

  • To model plant genome evolution using available EST collections.
  • To identify lineage-specific genes and gene families across plant species.

Main Methods:

  • Collated over four million ESTs from 50+ plant species into the openSputnik pipeline.
  • Resolved ESTs into approximately one million unigene sequences.
  • Annotated unigenes using orthology-based transfer and bioinformatics methods for functional attributes.

Main Results:

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  • The openSputnik database contains over one million unigenes from diverse plant species.
  • Annotation provided peptide, structural, and functional attributes for unigenes.
  • The data facilitates comparative genomics and evolutionary studies.

Conclusions:

  • EST collections are valuable resources for studying plant genome evolution.
  • The openSputnik database provides a comprehensive resource for plant gene analysis.
  • Comparative analysis of ESTs aids in understanding plant lineage-specific genes.