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Bioinformatics Vol. 19 no. 17 2003
pages 2191-2198
© 2003 Oxford University Press

Automatic design of gene-specific sequence tags for genome-wide functional studies

Vincent Thareau 1,3, Patrice Déhais 2,§, Carine Serizet 1,3, Pierre Hilson 2,3, Pierre Rouzé 1,* and Sébastien Aubourg 2,3

1 Laboratoire Associé de l'Institut National de Recherche Agronomique (France) and 2 Department of Plant Systems Biology, Flanders Interuniversity Institute of Biotechnology, Ghent University, Technologie Park 927, B-9052 Gent, Belgium and 3 Unité de Recherche en Génomique Végétale, UMR INRA-CNRS, 2, rue Gaston Crémieux, CP 5708, F-91057 Evry, France

Received on December 9, 2002 ; revised on March 6, 2003 ; accepted on May 8, 2003

Motivation: The availability of complete genome sequences allows the identification of short DNA segments that are specific to each annotated gene. Such unique gene sequence tags (GSTs) replace advantageously cDNAs in microarray transcript profiling experiments. In particular, probes corresponding to individual members of multigene families can be chosen carefully to avoid cross-hybridization events.

Results: The Specific Primer and Amplicon Design Software (SPADS) was constructed to delineate the more divergent regions in each gene by comparing them with a completely annotated genome sequence and to select optimal primer pairs for the polymerase chain reaction amplification of one divergent region per gene. SPADS is a unique integrated tool to design specific GSTs from any public or private genome sequences and allows the user to fine-tune GST size and specificity. SPADS has been used to obtain probes for whole genome and family-wide transcript profiling, as well as inserts for gene-specific knock-out experiments.

Availability: The GENOPLANTETM SPADS source code and web interface are available upon request. The online version is accessible via http://genoplante-info.infobiogen.fr/spads and via http://oberon.fvms.ugent.be:8080/SPADS/

Contact: pierre.rouze{at}psb.ugent.be

* To whom correspondence should be addressed.

§ Present address: INRA–AGENA, BP 27, F-31326 Castanet-Tolosan Cedex, France.


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