URL: | http://tools.ips2.u-psud.fr/FLAGdb |
Full name: | FLAGdb++ |
Description: | The FLAGdb++ application gives access to different plant genomes. Navigating between genomes is easy since they are stored in the same database instance. |
Year founded: | 2002 |
Last update: | 2018-4-20 |
Version: | v6.3 |
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Country/Region: | France |
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University/Institution: | Institute of Plant Sciences Paris-Saclay |
Address: | Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Sud, Univ Evry, Univ Paris-Saclay, Bâtiment 630, 91405, Orsay, France. |
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Country/Region: | France |
Contact name (PI/Team): | Véronique Brunaud |
Contact email (PI/Helpdesk): | Veronique.Brunaud@u-psud.fr |
FLAGdb++: A Bioinformatic Environment to Study and Compare Plant Genomes. [PMID: 27987165]
Today, the growing knowledge and data accumulation on plant genomes do not solve in a simple way the task of gene function inference. Because data of different types are coming from various sources, we need to integrate and analyze them to help biologists in this task. We created FLAGdb++ ( http://tools.ips2.u-psud.fr/FLAGdb ) to take up this challenge for a selection of plant genomes. In order to enrich gene function predictions, structural and functional annotations of the genomes are explored to generate meta-data and to compare them. Since data are numerous and complex, we focused on accessibility and visualization with an original and user-friendly interface. In this chapter we present the main tools of FLAGdb++ and a use-case to explore a gene family: structural and functional properties of this family and research of orthologous genes in the other plant genomes. |
Exploration of plant genomes in the FLAGdb++ environment. [PMID: 21447150]
BACKGROUND: In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas. |
FLAGdb++: a database for the functional analysis of the Arabidopsis genome. [PMID: 14681431]
FLAGdb++ is dedicated to the integration and visualization of data for high-throughput functional analysis of a fully sequenced genome, as illustrated for Arabidopsis. FLAGdb++ displays the predicted or experimental data in a position-dependent way and displays correlations and relationships between different features. FLAGdb++ provides for a given genome region, summarized characteristics of experimental materials like probe lengths, locations and specificities having an impact upon the confidence we will put in the experimental results. A selected subset of the available information is linked to a locus represented on an easy-to-interpret and memorable graphical display. Data are curated, processed and formatted before their integration into FLAGdb++. FLAGdb++ contains different options for easy back and forth navigation through many loci selected at the start of a session. It includes an original two-component visualization of the data, a genome-wide and a local view, which are permanently linked and display complementary information. Density curves along the chromosomes may be displayed in parallel for suggesting correlations between different structural and functional data. FLAGdb++ is fully accessible at http://genoplante-info.infobiogen.fr/FLAGdb/. |
FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants. [PMID: 11752264]
A large collection of T-DNA insertion transformants of Arabidopsis thaliana has been generated at the Institute of Agronomic Research, Versailles, France. The molecular characterisation of the insertion sites is currently performed by sequencing genomic regions flanking the inserted T-DNA (FST). The almost complete sequence of the nuclear genome of A.thaliana provides the framework for organising FSTs in a genome oriented database, FLAGdb/FST (http://genoplante-info.infobiogen.fr). The main scope of FLAGdb/FST is to help biologists to find the FSTs that interrupt the genes in which they are interested. FSTs are anchored to the genome sequences of A.thaliana and positions of both predicted genes and FSTs are shown graphically on sequences. Requests to locate the genomic position of a query sequence are made using BLAST programs. The response delivered by FLAGdb/FST is a graphical representation of the putative FSTs and of predicted genes in a 20 kb region. |