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Nucleic Acids Research, 2003, Vol. 31, No. 1 196-201
© 2003 Oxford University Press

MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome

Anne-Françoise J. Lamblin, John A. Crow, James E. Johnson, Kevin A. T. Silverstein1, Timothy M. Kunau, Alan Kilian, Diane Benz, Martina Stromvik, Gabriella Endré1, Kathryn A. VandenBosch1, Douglas R. Cook2, Nevin D. Young1 and Ernest F. Retzel*

Center for Computational Genomics and Bioinformatics, University of Minnesota, MMC43, 420 Delaware Street S.E., Minneapolis, MN 55455, USA 1 Department of Plant Biology, University of Minnesota, 220 Bio Sci Center, 1445 Gortner Avenue, St Paul, MN 55408, USA 2 Department of Plant Pathology, University of California, Davis, CA 95616, USA

*To whom correspondence should be addressed. Email: ernest{at}ccgb.umn.edu

ABSTRACT

In order to identify the genes and gene functions that underlie key aspects of legume biology, researchers have selected the cool season legume Medicago truncatula (Mt) as a model system for legume research. A set of >170 000 Mt ESTs has been assembled based on in-depth sampling from various developmental stages and pathogen-challenged tissues. MtDB is a relational database that integrates Mt transcriptome data and provides a wide range of user-defined data mining options. The database is interrogated through a series of interfaces with 58 options grouped into two filters. In addition, the user can select and compare unigene sets generated by different assemblers: Phrap, Cap3 and Cap4. Sequence identifiers from all public Mt sites (e.g. IDs from GenBank, CCGB, TIGR, NCGR, INRA) are fully cross-referenced to facilitate comparisons between different sites, and hypertext links to the appropriate database records are provided for all queries' results. MtDB's goal is to provide researchers with the means to quickly and independently identify sequences that match specific research interests based on user-defined criteria. The underlying database and query software have been designed for ease of updates and portability to other model organisms. Public access to the database is at http://www.medicago.org/MtDB.


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