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ForestTreeDB: a database dedicated to the mining of tree transcriptomes

ForestTreeDB is intended as a resource that centralizes large-scale expressed sequence tag (EST) sequencing results from several tree species (). It currently encompasses 344 878 quality sequences from 68 libraries, from diverse organs of conifer and hybrid poplar trees. It utilizes the Nimbus data...

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Autores principales: Pavy, Nathalie, Johnson, James J., Crow, John A., Paule, Charles, Kunau, Timothy, MacKay, John, Retzel, Ernest F.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716727/
https://www.ncbi.nlm.nih.gov/pubmed/17130142
http://dx.doi.org/10.1093/nar/gkl882
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author Pavy, Nathalie
Johnson, James J.
Crow, John A.
Paule, Charles
Kunau, Timothy
MacKay, John
Retzel, Ernest F.
author_facet Pavy, Nathalie
Johnson, James J.
Crow, John A.
Paule, Charles
Kunau, Timothy
MacKay, John
Retzel, Ernest F.
author_sort Pavy, Nathalie
collection PubMed
description ForestTreeDB is intended as a resource that centralizes large-scale expressed sequence tag (EST) sequencing results from several tree species (). 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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spelling pubmed-17167272007-02-22 ForestTreeDB: a database dedicated to the mining of tree transcriptomes Pavy, Nathalie Johnson, James J. Crow, John A. Paule, Charles Kunau, Timothy MacKay, John Retzel, Ernest F. Nucleic Acids Res Articles ForestTreeDB is intended as a resource that centralizes large-scale expressed sequence tag (EST) sequencing results from several tree species (). 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. Oxford University Press 2007-01 2006-11-27 /pmc/articles/PMC1716727/ /pubmed/17130142 http://dx.doi.org/10.1093/nar/gkl882 Text en © 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.
spellingShingle Articles
Pavy, Nathalie
Johnson, James J.
Crow, John A.
Paule, Charles
Kunau, Timothy
MacKay, John
Retzel, Ernest F.
ForestTreeDB: a database dedicated to the mining of tree transcriptomes
title ForestTreeDB: a database dedicated to the mining of tree transcriptomes
title_full ForestTreeDB: a database dedicated to the mining of tree transcriptomes
title_fullStr ForestTreeDB: a database dedicated to the mining of tree transcriptomes
title_full_unstemmed ForestTreeDB: a database dedicated to the mining of tree transcriptomes
title_short ForestTreeDB: a database dedicated to the mining of tree transcriptomes
title_sort foresttreedb: a database dedicated to the mining of tree transcriptomes
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716727/
https://www.ncbi.nlm.nih.gov/pubmed/17130142
http://dx.doi.org/10.1093/nar/gkl882
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