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Database Commons - ForestTreeDB

ForestTreeDB

Citations: 29

z-index 1.48

Short name ForestTreeDB
Full name ForestTreeDB
Description ForestTreeDB is intended as a resource that centralizes large-scale expressed sequence tag (EST) sequencing results from several tree species.
URL http://foresttree.org/ftdb
Year founded 2007
Last update & version     
Availability Not Available
University/Institution hosted Laval University
Address Laval University, Centre de Recherche en Biologie Forestière, Québec, Canada
City Québec
Province/State
Country/Region Canada
Contact name Nathalie Pavy
Contact email nathalie.pavy@rsvs.ulaval.ca
Data type(s)
Major organism(s)
Keyword(s)
  • Expressed Sequence Tag (EST)
  • tree
Publication(s)
  • ForestTreeDB: a database dedicated to the mining of tree transcriptomes. [PMID: 17130142]

    Nathalie Pavy, James J Johnson, John A Crow, Charles Paule, Timothy Kunau, John MacKay, Ernest F Retzel
    Nucleic acids research 2007:35(Database issue)
    29 Citations (Google Scholar as of 2016-05-02)

    Abstract: 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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Accessibility

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Tags

DNA Expression RNA
Plant
Expressed Sequence Tag (EST) tree

Record metadata

  • Created on: 2015-08-10
  • Curated by:
    • Lina Ma [2016-08-16]
    • Zhang Zhang [2016-05-08]
    • Lina Ma [2016-04-08]
    • Jian Sang [2016-04-03]
    • Mengwei Li [2016-02-21]
    • Lina Ma [2015-12-31]
Stats