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Nucleic Acids Research Advance Access published online on November 27, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl882
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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

ForestTreeDB: a database dedicated to the mining of tree transcriptomes

Nathalie Pavy1,*, James J. Johnson1, John A. Crow1, Charles Paule1, Timothy Kunau1, John MacKay and Ernest F. Retzel2,3

1 Laval University, Centre de Recherche en Biologie Forestière Québec, Canada G1K 7P4 2 University of Minnesota, CCGB Minneapolis, MN, USA 3 University MN, AHC-Research Computing 426 Church Street SE, Minneapolis, MN 55455, USA

*To whom correspondence should be addressed at: Laval University, Centre de recherche en biologie forestière, Pavillon C.E. Marchand, Québec, Canada G1K 7P4. Tel: +1 418 656 2131; Fax: +1 418 656 793; Email: nathalie.pavy{at}rsvs.ulaval.ca

Received August 16, 2006. Revised October 10, 2006. Accepted October 11, 2006.

ForestTreeDB is intended as a resource that centralizes large-scale expressed sequence tag (EST) sequencing results from several tree species (http://foresttree.org/ftdb). It currently encompasses 344 878 quality sequences from 68 libraries, from diverse organs of conifer and hybrid poplar trees. It utilizes the Nimbus data model to provide a hosting system for multiple projects, and uses object-relational mapping APIs in Java and Perl for data accesses within an Oracle database designed to be scalable, maintainable and extendable. Transcriptome builds or unigene sets occupy the focal point of the system. Several of the five current species-specific unigenes were used to design microarrays and SNP resources. The ForestTreeDB web application provides the means for multiple combination database queries. It presents the user with a list of discrete queries to retrieve and download large EST datasets or sequences from precompiled unigene assemblies. Functional annotation assignment is not trivial in conifers which are distantly related to angiosperm model plants. Optimal annotations are achieved through database queries that integrate results from several procedures based open-source tools. ForestTreeDB aims to facilitate sequence mining of coherent annotations in multiple species to support comparative genomic approaches. We plan to continuously enrich ForestTreeDB with other resources through collaborations with other genomic projects.


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