Nucleic Acids Research, 2005, Vol. 33, Database issue D622-D627
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
openSputnik—a database to ESTablish comparative plant genomics using unsaturated sequence collections
Centre for Biotechnology, Tykistökatu 6, FIN-20521 Turku, Finland
* Tel: +358 0 2 333 8611; Fax: +358 0 2 333 8000; Email: stephen.rudd{at}btk.utu.fi
Received September 15, 2004; Revised and Accepted September 27, 2004
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.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  P. K. Wall, J. Leebens-Mack, K. F. Muller, D. Field, N. S. Altman, and C. W. dePamphilis PlantTribes: a gene and gene family resource for comparative genomics in plants Nucleic Acids Res., January 11, 2008; 36(suppl_1): D970 - D976. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Hartmann, D. Lu, J. Phillips, and T. J. Vision Phytome: a platform for plant comparative genomics Nucleic Acids Res., January 1, 2006; 34(suppl_1): D724 - D730. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Rudd and I. V. Tetko Eclair--a web service for unravelling species origin of sequences sampled from mixed host interfaces Nucleic Acids Res., July 1, 2005; 33(suppl_2): W724 - W727. [Abstract] [Full Text] [PDF]
|
|