Tomato gene expression database
TomatEST is a secondary database integrating EST/cDNA sequence information from different libraries of multiple tomato species collected from dbEST. 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.
This work is supported by the AGRONANOTECH project (Italian Ministry of Agriculture) and by the EU-SOL project (VI frame programme of the European Community).
We thank Dr. Alessandra Traini and Dr. Enrico Raimondo for useful feedback on the database usage. We thank Prof. Gerardo Toraldo for technical support and useful discussions.