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Nucleic Acids Research 2005 33(Database Issue):D628-D632; doi:10.1093/nar/gki074
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Nucleic Acids Research, 2005, Vol. 33, Database issue D628-D632
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

PlantMarkers—a database of predicted molecular markers from plants

Stephen Rudd1,*, Heiko Schoof2,3 and Klaus Mayer3

1 Centre for Biotechnology, Tykistökatu 6, FIN-20521 Turku, Finland, 2 Technische Universität München, Chair of Genome Oriented Bioinformatics, D-85350 Fresing-Weihenstephan, Germany and 3 Institute for Bioinformatics (MIPS), GSF Research Centre for Environment and Health, D-85764 Neuherberg, Germany

* To whom correspondence should be addressed. Tel: +358 2 333 8611; Fax: +358 2 333 8000; Email: stephen.rudd{at}btk.utu.fi

Received August 15, 2004; Revised and Accepted October 8, 2004

Molecular markers are required in a broad spectrum of gene screening approaches, ranging from gene-mapping within traditional ‘forward’-genetics approaches through QTL identification studies to genotyping and haplotyping studies. As we enter the post-genomics era, the need for genetic markers does not diminish, even in the species with fully sequenced genomes. PlantMarkers is a genetic marker database that contains a comprehensive pool of predicted molecular markers. We have adopted contemporary techniques to identify putative single nucleotide polymorphism (SNP), simple sequence repeat (SSR) and conserved orthologue set markers. A systematic approach to identify as broad a range of putative markers has been undertaken by screening the available openSputnik unigene consensus sequences from over 50 plant species. A web presence at http://markers.btk.fi provides functionality so that a user may search for species-specific markers on the basis of many specific criteria not limited to non-synonymous SNPs segregating between different varieties or measured polymorphic SSRs. Feedback forms are provided with all sequence entries to enable inclusion of, for example, map location for markers validated by the research community.

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