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Nucleic Acids Research 2006 34(Web Server issue):W670-W675; doi:10.1093/nar/gkl201
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© The Author 2006. Published by Oxford University Press. All rights reserved
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, please contact journals.permissions@oxfordjournals.org

Article

GeMprospector—online design of cross-species genetic marker candidates in legumes and grasses

Jakob Fredslund*, Lene H. Madsen1, Birgit K. Hougaard1, Niels Sandal1, Jens Stougaard1, David Bertioli2 and Leif Schauser

Bioinformatics Research Centre, University of Aarhus Høegh-Guldbergsgade 10, 8000 Aarhus C, Denmark 1 Laboratory of Gene Expression, Department of Molecular Biology, University of Aarhus Gustav Wieds Vej 10, 8000 Aarhus C, Denmark 2 Univerisidade Catolica de Brasil, UCB, Programa de Pós-Graduação em Biotecnologia Genômica Campus II, SGAN Quadra 916, Módulo B, Avenue W5 Norte, Brasília, DF, CEP: 70790-160, Brazil

*To whom correspondence should be addressed. Tel: +45 8942 3125; Fax: +45 8942 3077; Email: jakobf{at}birc.au.dk

Received February 13, 2006. Revised March 22, 2006. Accepted March 22, 2006.

The web program GeMprospector (URL: http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main) allows users to automatically design large sets of cross-species genetic marker candidates targeting either legumes or grasses. The user uploads a collection of ESTs from one or more legume or grass species, and they are compared with a database of clusters of homologous EST and genomic sequences from other legumes or grasses, respectively. Multiple sequence alignments between submitted ESTs and their homologues in the appropriate database form the basis of automated PCR primer design in conserved exons such that each primer set amplifies an intron. The only user input is a collection of ESTs, not necessarily from more than one species, and GeMprospector can boost the potential of such an EST collection by combining it with a large database to produce cross-species genetic marker candidates for legumes or grasses.


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