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PkGDB : Prokaryotic Genome DataBase

MaGe - Magnifying Genomes
MaGe : a bacterial genomes annotation system


The implementation of IT (Information Technology) resources required to extract meaningful information from data of micro-organisms genomes currently available, or under sequencing process, needs the development of specific methods, more complex analysis strategies, specialized databases, or websites offering free access to these methods and these databases.

Development of annotation & analysis tools

The annotation of prokaryotic genome refers to three main objectives that are developed within the LABGeM team:
- Syntactic annotation concerns the identification of regions of interest on the sequence (genes, signals, etc..).
- Functional annotation for the allocation of one (or several) biological(s) function(s) to the signals previously detected.
- Relational annotation seeks to identify the cellular and physiological processes, i.e to determine how genes and proteins interact to accomplish a specific task in the cell.

Development of relational databases

Our group hold since several years a relational database with the Database Management System MySQL (Open Source licensed): Procaryotic Genome DataBase (PkGDB). The generic structure of the database is used to model data from a set of bacterial genomes. This data is needed for both annotation and re-annotation of genomes.

Development of a platform dedicated to annotation: MicroScope & MaGe system

If the automatic analysis of a newly sequenced genome and «smart» storage results are essential steps in syntactic & functional annotation process, it is equally crucial to have a graphical interface that allows quick access to essential information of each gene annotations in order to carry out the expert annotation of genes. This need was quickly generated by the sequencing of the bacterium Acinetobacter ADP1 at Genoscope.

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