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Nucleic Acids Research Advance Access published online on November 16, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl921
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species

Nunzio D'Agostino, Mario Aversano, Luigi Frusciante1 and Maria Luisa Chiusano*

Department of Structural and Functional Biology, University ‘Federico II’ 80126 Naples, Italy 1 Department of Soil, Plant and Environmental Sciences, University ‘Federico II’, 80055 Portici, Naples, Italy

*To whom correspondence should be addressed. Tel/Fax: +39 081679186; Email: chiusano{at}unina.it

Received August 1, 2006. Accepted October 17, 2006.

TomatEST is a secondary database integrating expressed sequence tag (EST)/cDNA sequence information from different libraries of multiple tomato species. Redundant EST collections from each species are organized into clusters (gene indices). A cluster consists of one or multiple contigs. Multiple contigs in a cluster represent alternatively transcribed forms of a gene. The set of stand-alone EST sequences (singletons) and contigs, representing all the computationally defined ‘Transcript Indices’, are annotated according to similarity versus protein and RNA family databases. Sequence function description is integrated with the Gene Ontologies and the Enzyme Commission identifiers for a standard classification of gene products and for the mapping of the expressed sequences onto metabolic pathways. Information on the origin of the ESTs, on their structural features, on clusters and contigs, as well as on functional annotations are accessible via a user-friendly web interface. Specific facilities in the database allow Transcript Indices from a query be automatically classified in Enzyme classes and in metabolic pathways. The ‘on the fly’ mapping onto the metabolic maps is integrated in the analytical tools. The TomatEST database website is freely available at http://biosrv.cab.unina.it/tomatestdb.


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