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Nucleic Acids Research, 2003, Vol. 31, No. 1 128-132
© 2003 Oxford University Press

Sputnik: a database platform for comparative plant genomics

Stephen Rudd*,1, Hans-Werner Mewes1,2 and Klaus F.X. Mayer1

1 Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany 2 Department of Genome-Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85350 Freising, Germany

*To whom correspondence should be addressed. Fax: +49 8931873585; Email: s.rudd{at}gsf.de

ABSTRACT

Two million plant ESTs, from 20 different plant species, and totalling more than one 1000 Mbp of DNA sequence, represents a formidable transcriptomic resource. Sputnik uses the potential of this sequence resource to fill some of the information gap in the un-sequenced plant genomes and to serve as the foundation for in silicio comparative plant genomics. The complexity of the individual EST collections has been reduced using optimised EST clustering techniques. Annotation of cluster sequences is performed by exploiting and transferring information from the comprehensive knowledgebase already produced for the completed model plant genome (Arabidopsis thaliana) and by performing additional state of-the-art sequence analyses relevant to today's plant biologist. Functional predictions, comparative analyses and associative annotations for 500 000 plant EST derived peptides make Sputnik (http://mips.gsf.de/proj/sputnik/) a valid platform for contemporary plant genomics.


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