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Database Commons - openSputnik

openSputnik

Citations: 28

z-index 0.00

Short name openSputnik
Full name A database to ESTablish comparative plant genomics
Description openSputnik--a database to ESTablish comparative plant genomics using unsaturated sequence collections.
URL http://sputnik.btk.fi
Year founded 2004
Last update & version 2004-12-17    
Availability Not Available
University/Institution hosted Centre for Biotechnology
Address Tykistökatu 6, FIN-20521 Turku, Finland
City Turku
Province/State
Country/Region Finland
Contact name Stephen Rudd
Contact email stephen.rudd@btk.utu.fi
Data type(s)
Major organism(s)
Keyword(s)
  • EST
Publication(s)
  • openSputnik--a database to ESTablish comparative plant genomics using unsaturated sequence collections. [PMID: 15608275]

    Stephen Rudd
    Nucleic acids research 2005:33(Database issue)
    28 Citations (Google Scholar as of 2016-03-02)

    Abstract: The public expressed sequence tag collections are continually being enriched with high-quality sequences that represent an ever-expanding range of taxonomically diverse plant species. While these sequence collections provide biased insight into the populations of expressed genes available within individual species and their associated tissues, the information is conceivably of wider relevance in a comparative context. When we consider the available expressed sequence tag (EST) collections of summer 2004, most of the major plant taxonomic clades are at least superficially represented. Investigation of the five million available plant ESTs provides a wealth of information that has applications in modelling the routes of plant genome evolution and the identification of lineage-specific genes and gene families. Over four million ESTs from over 50 distinct plant species have been collated within an EST analysis pipeline called openSputnik. The ESTs were resolved down into approximately one million unigene sequences. These have been annotated using orthology-based annotation transfer from reference plant genomes and using a variety of contemporary bioinformatics methods to assign peptide, structural and functional attributes. The openSputnik database is available at http://sputnik.btk.fi.

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Tags

Expression
Plant
EST

Record metadata

  • Created on: 2015-07-14
  • Curated by:
    • Lin Liu [2016-03-30]
    • Lin Liu [2016-03-28]
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